Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 26 17:35:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/08_2023/6bgo_7098_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 29149 2.51 5 N 8249 2.21 5 O 8990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 433": "OE1" <-> "OE2" Residue "P GLU 434": "OE1" <-> "OE2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "P GLU 512": "OE1" <-> "OE2" Residue "Q GLU 433": "OE1" <-> "OE2" Residue "Q GLU 434": "OE1" <-> "OE2" Residue "Q ARG 488": "NH1" <-> "NH2" Residue "Q GLU 512": "OE1" <-> "OE2" Residue "R GLU 433": "OE1" <-> "OE2" Residue "R GLU 434": "OE1" <-> "OE2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "R GLU 512": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 434": "OE1" <-> "OE2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "S GLU 512": "OE1" <-> "OE2" Residue "T GLU 433": "OE1" <-> "OE2" Residue "T GLU 434": "OE1" <-> "OE2" Residue "T ARG 488": "NH1" <-> "NH2" Residue "T GLU 512": "OE1" <-> "OE2" Residue "U GLU 433": "OE1" <-> "OE2" Residue "U GLU 434": "OE1" <-> "OE2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "U GLU 512": "OE1" <-> "OE2" Residue "V GLU 433": "OE1" <-> "OE2" Residue "V GLU 434": "OE1" <-> "OE2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "V GLU 512": "OE1" <-> "OE2" Residue "W GLU 433": "OE1" <-> "OE2" Residue "W GLU 434": "OE1" <-> "OE2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "W GLU 512": "OE1" <-> "OE2" Residue "X GLU 433": "OE1" <-> "OE2" Residue "X GLU 434": "OE1" <-> "OE2" Residue "X ARG 488": "NH1" <-> "NH2" Residue "X GLU 512": "OE1" <-> "OE2" Residue "Y GLU 433": "OE1" <-> "OE2" Residue "Y GLU 434": "OE1" <-> "OE2" Residue "Y ARG 488": "NH1" <-> "NH2" Residue "Y GLU 512": "OE1" <-> "OE2" Residue "Z GLU 433": "OE1" <-> "OE2" Residue "Z GLU 434": "OE1" <-> "OE2" Residue "Z ARG 488": "NH1" <-> "NH2" Residue "Z GLU 512": "OE1" <-> "OE2" Residue "a GLU 433": "OE1" <-> "OE2" Residue "a GLU 434": "OE1" <-> "OE2" Residue "a ARG 488": "NH1" <-> "NH2" Residue "a GLU 512": "OE1" <-> "OE2" Residue "b GLU 433": "OE1" <-> "OE2" Residue "b GLU 434": "OE1" <-> "OE2" Residue "b ARG 488": "NH1" <-> "NH2" Residue "b GLU 512": "OE1" <-> "OE2" Residue "c GLU 433": "OE1" <-> "OE2" Residue "c GLU 434": "OE1" <-> "OE2" Residue "c ARG 488": "NH1" <-> "NH2" Residue "c GLU 512": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 46500 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "D" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "E" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "F" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "G" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "I" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1658 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Chain: "J" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1673 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1678 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Q" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "R" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "S" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "T" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1636 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "V" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "W" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "X" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Y" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "Z" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "a" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "b" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1638 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "d" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "e" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "f" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "g" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "h" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "i" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Chain: "j" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Classifications: {'peptide': 4} Modifications used: {'COO': 1} Link IDs: {'TRANS': 3} Time building chain proxies: 23.14, per 1000 atoms: 0.50 Number of scatterers: 46500 At special positions: 0 Unit cell: (138.43, 147.15, 178.76, 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 112 16.00 O 8990 8.00 N 8249 7.00 C 29149 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: 18.65 Conformation dependent library (CDL) restraints added in 7.0 seconds 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11206 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 72 sheets defined 47.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 95 through 114 Processing helix chain 'A' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU A 230 " --> pdb=" O THR A 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 95 through 114 Processing helix chain 'C' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 190 Processing helix chain 'C' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU C 230 " --> pdb=" O THR C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR D 84 " --> pdb=" O GLN D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 95 through 114 Processing helix chain 'D' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 190 Processing helix chain 'D' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU D 230 " --> pdb=" O THR D 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 26 Processing helix chain 'E' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR E 84 " --> pdb=" O GLN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 95 through 114 Processing helix chain 'E' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 190 Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU E 230 " --> pdb=" O THR E 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 26 Processing helix chain 'F' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR F 84 " --> pdb=" O GLN F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 95 through 114 Processing helix chain 'F' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 190 Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU F 230 " --> pdb=" O THR F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 Processing helix chain 'G' and resid 68 through 89 removed outlier: 3.516A pdb=" N THR G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 95 through 114 Processing helix chain 'G' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 190 Processing helix chain 'G' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU G 230 " --> pdb=" O THR G 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 26 Processing helix chain 'H' and resid 67 through 89 removed outlier: 3.516A pdb=" N THR H 84 " --> pdb=" O GLN H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 95 through 114 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 190 Processing helix chain 'H' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU H 230 " --> pdb=" O THR H 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 26 Processing helix chain 'I' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR I 84 " --> pdb=" O GLN I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 95 through 114 Processing helix chain 'I' and resid 159 through 171 removed outlier: 4.612A pdb=" N ILE I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 190 Processing helix chain 'I' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU I 230 " --> pdb=" O THR I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 26 Processing helix chain 'J' and resid 67 through 89 removed outlier: 3.517A pdb=" N THR J 84 " --> pdb=" O GLN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 94 Processing helix chain 'J' and resid 95 through 114 Processing helix chain 'J' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 190 Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU J 230 " --> pdb=" O THR J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 26 Processing helix chain 'K' and resid 67 through 89 removed outlier: 3.517A pdb=" N THR K 84 " --> pdb=" O GLN K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 94 Processing helix chain 'K' and resid 95 through 114 Processing helix chain 'K' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 226 through 234 removed outlier: 3.912A pdb=" N LEU K 230 " --> pdb=" O THR K 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 26 Processing helix chain 'L' and resid 67 through 89 removed outlier: 3.514A pdb=" N THR L 84 " --> pdb=" O GLN L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 94 Processing helix chain 'L' and resid 95 through 114 Processing helix chain 'L' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 190 Processing helix chain 'L' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 26 Processing helix chain 'M' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR M 84 " --> pdb=" O GLN M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 90 through 94 Processing helix chain 'M' and resid 95 through 114 Processing helix chain 'M' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE M 163 " --> pdb=" O THR M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 190 Processing helix chain 'M' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU M 230 " --> pdb=" O THR M 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 26 Processing helix chain 'N' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR N 84 " --> pdb=" O GLN N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 94 Processing helix chain 'N' and resid 95 through 114 Processing helix chain 'N' and resid 159 through 171 removed outlier: 4.610A pdb=" N ILE N 163 " --> pdb=" O THR N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 Processing helix chain 'N' and resid 226 through 234 removed outlier: 3.910A pdb=" N LEU N 230 " --> pdb=" O THR N 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 8 through 26 Processing helix chain 'O' and resid 67 through 89 removed outlier: 3.515A pdb=" N THR O 84 " --> pdb=" O GLN O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 94 Processing helix chain 'O' and resid 95 through 114 Processing helix chain 'O' and resid 159 through 171 removed outlier: 4.611A pdb=" N ILE O 163 " --> pdb=" O THR O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 190 Processing helix chain 'O' and resid 226 through 234 removed outlier: 3.911A pdb=" N LEU O 230 " --> pdb=" O THR O 226 " (cutoff:3.500A) Processing helix chain 'P' and resid 348 through 371 Processing helix chain 'P' and resid 375 through 390 Processing helix chain 'P' and resid 390 through 396 Processing helix chain 'P' and resid 413 through 416 Processing helix chain 'P' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS P 452 " --> pdb=" O SER P 448 " (cutoff:3.500A) Processing helix chain 'P' and resid 455 through 457 No H-bonds generated for 'chain 'P' and resid 455 through 457' Processing helix chain 'P' and resid 459 through 478 Processing helix chain 'P' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE P 510 " --> pdb=" O PRO P 506 " (cutoff:3.500A) Processing helix chain 'Q' and resid 348 through 371 Processing helix chain 'Q' and resid 375 through 390 Processing helix chain 'Q' and resid 390 through 396 Processing helix chain 'Q' and resid 413 through 416 Processing helix chain 'Q' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Q 452 " --> pdb=" O SER Q 448 " (cutoff:3.500A) Processing helix chain 'Q' and resid 455 through 457 No H-bonds generated for 'chain 'Q' and resid 455 through 457' Processing helix chain 'Q' and resid 459 through 478 Processing helix chain 'Q' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Q 510 " --> pdb=" O PRO Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 348 through 371 Processing helix chain 'R' and resid 375 through 390 Processing helix chain 'R' and resid 390 through 396 Processing helix chain 'R' and resid 413 through 416 Processing helix chain 'R' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS R 452 " --> pdb=" O SER R 448 " (cutoff:3.500A) Processing helix chain 'R' and resid 455 through 457 No H-bonds generated for 'chain 'R' and resid 455 through 457' Processing helix chain 'R' and resid 459 through 478 Processing helix chain 'R' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE R 510 " --> pdb=" O PRO R 506 " (cutoff:3.500A) Processing helix chain 'S' and resid 348 through 371 Processing helix chain 'S' and resid 375 through 390 Processing helix chain 'S' and resid 390 through 396 Processing helix chain 'S' and resid 413 through 416 Processing helix chain 'S' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS S 452 " --> pdb=" O SER S 448 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 457 No H-bonds generated for 'chain 'S' and resid 455 through 457' Processing helix chain 'S' and resid 459 through 478 Processing helix chain 'S' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE S 510 " --> pdb=" O PRO S 506 " (cutoff:3.500A) Processing helix chain 'T' and resid 348 through 371 Processing helix chain 'T' and resid 375 through 390 Processing helix chain 'T' and resid 390 through 396 Processing helix chain 'T' and resid 413 through 416 Processing helix chain 'T' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS T 452 " --> pdb=" O SER T 448 " (cutoff:3.500A) Processing helix chain 'T' and resid 455 through 457 No H-bonds generated for 'chain 'T' and resid 455 through 457' Processing helix chain 'T' and resid 459 through 478 Processing helix chain 'T' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE T 510 " --> pdb=" O PRO T 506 " (cutoff:3.500A) Processing helix chain 'U' and resid 348 through 371 Processing helix chain 'U' and resid 375 through 390 Processing helix chain 'U' and resid 390 through 396 Processing helix chain 'U' and resid 413 through 416 Processing helix chain 'U' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS U 452 " --> pdb=" O SER U 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 455 through 457 No H-bonds generated for 'chain 'U' and resid 455 through 457' Processing helix chain 'U' and resid 459 through 478 Processing helix chain 'U' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE U 510 " --> pdb=" O PRO U 506 " (cutoff:3.500A) Processing helix chain 'V' and resid 348 through 371 Processing helix chain 'V' and resid 375 through 390 Processing helix chain 'V' and resid 390 through 396 Processing helix chain 'V' and resid 413 through 416 Processing helix chain 'V' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS V 452 " --> pdb=" O SER V 448 " (cutoff:3.500A) Processing helix chain 'V' and resid 455 through 457 No H-bonds generated for 'chain 'V' and resid 455 through 457' Processing helix chain 'V' and resid 459 through 478 Processing helix chain 'V' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE V 510 " --> pdb=" O PRO V 506 " (cutoff:3.500A) Processing helix chain 'W' and resid 348 through 371 Processing helix chain 'W' and resid 375 through 390 Processing helix chain 'W' and resid 390 through 396 Processing helix chain 'W' and resid 413 through 416 Processing helix chain 'W' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS W 452 " --> pdb=" O SER W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 455 through 457 No H-bonds generated for 'chain 'W' and resid 455 through 457' Processing helix chain 'W' and resid 459 through 478 Processing helix chain 'W' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE W 510 " --> pdb=" O PRO W 506 " (cutoff:3.500A) Processing helix chain 'X' and resid 348 through 371 Processing helix chain 'X' and resid 375 through 390 Processing helix chain 'X' and resid 390 through 396 Processing helix chain 'X' and resid 413 through 416 Processing helix chain 'X' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS X 452 " --> pdb=" O SER X 448 " (cutoff:3.500A) Processing helix chain 'X' and resid 455 through 457 No H-bonds generated for 'chain 'X' and resid 455 through 457' Processing helix chain 'X' and resid 459 through 478 Processing helix chain 'X' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE X 510 " --> pdb=" O PRO X 506 " (cutoff:3.500A) Processing helix chain 'Y' and resid 348 through 371 Processing helix chain 'Y' and resid 375 through 390 Processing helix chain 'Y' and resid 390 through 396 Processing helix chain 'Y' and resid 413 through 416 Processing helix chain 'Y' and resid 442 through 454 removed outlier: 4.022A pdb=" N LYS Y 452 " --> pdb=" O SER Y 448 " (cutoff:3.500A) Processing helix chain 'Y' and resid 455 through 457 No H-bonds generated for 'chain 'Y' and resid 455 through 457' Processing helix chain 'Y' and resid 459 through 478 Processing helix chain 'Y' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE Y 510 " --> pdb=" O PRO Y 506 " (cutoff:3.500A) Processing helix chain 'Z' and resid 348 through 371 Processing helix chain 'Z' and resid 375 through 390 Processing helix chain 'Z' and resid 390 through 396 Processing helix chain 'Z' and resid 413 through 416 Processing helix chain 'Z' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS Z 452 " --> pdb=" O SER Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 455 through 457 No H-bonds generated for 'chain 'Z' and resid 455 through 457' Processing helix chain 'Z' and resid 459 through 478 Processing helix chain 'Z' and resid 506 through 522 removed outlier: 3.835A pdb=" N ILE Z 510 " --> pdb=" O PRO Z 506 " (cutoff:3.500A) Processing helix chain 'a' and resid 348 through 371 Processing helix chain 'a' and resid 375 through 390 Processing helix chain 'a' and resid 390 through 396 Processing helix chain 'a' and resid 413 through 416 Processing helix chain 'a' and resid 442 through 454 removed outlier: 4.023A pdb=" N LYS a 452 " --> pdb=" O SER a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 455 through 457 No H-bonds generated for 'chain 'a' and resid 455 through 457' Processing helix chain 'a' and resid 459 through 478 Processing helix chain 'a' and resid 506 through 522 removed outlier: 3.835A pdb=" N ILE a 510 " --> pdb=" O PRO a 506 " (cutoff:3.500A) Processing helix chain 'b' and resid 348 through 371 Processing helix chain 'b' and resid 375 through 390 Processing helix chain 'b' and resid 390 through 396 Processing helix chain 'b' and resid 413 through 416 Processing helix chain 'b' and resid 442 through 454 removed outlier: 4.022A pdb=" N LYS b 452 " --> pdb=" O SER b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 455 through 457 No H-bonds generated for 'chain 'b' and resid 455 through 457' Processing helix chain 'b' and resid 459 through 478 Processing helix chain 'b' and resid 506 through 522 removed outlier: 3.834A pdb=" N ILE b 510 " --> pdb=" O PRO b 506 " (cutoff:3.500A) Processing helix chain 'c' and resid 348 through 371 Processing helix chain 'c' and resid 375 through 390 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 413 through 416 Processing helix chain 'c' and resid 442 through 454 removed outlier: 4.024A pdb=" N LYS c 452 " --> pdb=" O SER c 448 " (cutoff:3.500A) Processing helix chain 'c' and resid 455 through 457 No H-bonds generated for 'chain 'c' and resid 455 through 457' Processing helix chain 'c' and resid 459 through 478 Processing helix chain 'c' and resid 506 through 522 removed outlier: 3.833A pdb=" N ILE c 510 " --> pdb=" O PRO c 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 156 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU A 138 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL C 60 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 138 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AA6, first strand: chain 'D' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL D 60 " --> pdb=" O LEU D 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU D 138 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 153 through 156 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 6.496A pdb=" N VAL E 60 " --> pdb=" O LEU E 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 138 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 138 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 153 through 156 Processing sheet with id=AB4, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU G 138 " --> pdb=" O GLU G 150 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL G 60 " --> pdb=" O LEU G 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU H 138 " --> pdb=" O GLU H 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 153 through 156 Processing sheet with id=AB9, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL I 60 " --> pdb=" O LEU I 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU I 138 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 153 through 156 Processing sheet with id=AC2, first strand: chain 'J' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU J 138 " --> pdb=" O GLU J 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 153 through 156 Processing sheet with id=AC4, first strand: chain 'K' and resid 53 through 57 removed outlier: 6.494A pdb=" N VAL K 60 " --> pdb=" O LEU K 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU K 138 " --> pdb=" O GLU K 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 153 through 156 Processing sheet with id=AC6, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU L 138 " --> pdb=" O GLU L 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 153 through 156 Processing sheet with id=AC8, first strand: chain 'M' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU M 138 " --> pdb=" O GLU M 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 153 through 156 Processing sheet with id=AD1, first strand: chain 'N' and resid 53 through 57 removed outlier: 6.495A pdb=" N VAL N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU N 138 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 153 through 156 Processing sheet with id=AD3, first strand: chain 'O' and resid 53 through 57 removed outlier: 6.493A pdb=" N VAL O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU O 138 " --> pdb=" O GLU O 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 436 through 439 Processing sheet with id=AD5, first strand: chain 'P' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER P 320 " --> pdb=" O SER P 327 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR P 341 " --> pdb=" O THR P 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE P 423 " --> pdb=" O PRO P 402 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 436 through 439 Processing sheet with id=AD8, first strand: chain 'Q' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER Q 320 " --> pdb=" O SER Q 327 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Q 341 " --> pdb=" O THR Q 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE Q 423 " --> pdb=" O PRO Q 402 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 436 through 439 Processing sheet with id=AE2, first strand: chain 'R' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER R 320 " --> pdb=" O SER R 327 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR R 341 " --> pdb=" O THR R 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE R 423 " --> pdb=" O PRO R 402 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 436 through 439 Processing sheet with id=AE5, first strand: chain 'S' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER S 320 " --> pdb=" O SER S 327 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR S 341 " --> pdb=" O THR S 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE S 423 " --> pdb=" O PRO S 402 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 436 through 439 Processing sheet with id=AE8, first strand: chain 'T' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER T 320 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR T 341 " --> pdb=" O THR T 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE T 423 " --> pdb=" O PRO T 402 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'U' and resid 436 through 439 Processing sheet with id=AF2, first strand: chain 'U' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER U 320 " --> pdb=" O SER U 327 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 334 through 338 removed outlier: 6.497A pdb=" N THR U 341 " --> pdb=" O THR U 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE U 423 " --> pdb=" O PRO U 402 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 436 through 439 Processing sheet with id=AF5, first strand: chain 'V' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER V 320 " --> pdb=" O SER V 327 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 334 through 338 removed outlier: 6.494A pdb=" N THR V 341 " --> pdb=" O THR V 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE V 423 " --> pdb=" O PRO V 402 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'W' and resid 436 through 439 Processing sheet with id=AF8, first strand: chain 'W' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER W 320 " --> pdb=" O SER W 327 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR W 341 " --> pdb=" O THR W 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE W 423 " --> pdb=" O PRO W 402 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X' and resid 436 through 439 Processing sheet with id=AG2, first strand: chain 'X' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER X 320 " --> pdb=" O SER X 327 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR X 341 " --> pdb=" O THR X 337 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE X 423 " --> pdb=" O PRO X 402 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Y' and resid 436 through 439 Processing sheet with id=AG5, first strand: chain 'Y' and resid 320 through 322 removed outlier: 6.386A pdb=" N SER Y 320 " --> pdb=" O SER Y 327 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR Y 341 " --> pdb=" O THR Y 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE Y 423 " --> pdb=" O PRO Y 402 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 436 through 439 Processing sheet with id=AG8, first strand: chain 'Z' and resid 320 through 322 removed outlier: 6.385A pdb=" N SER Z 320 " --> pdb=" O SER Z 327 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR Z 341 " --> pdb=" O THR Z 337 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE Z 423 " --> pdb=" O PRO Z 402 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'a' and resid 436 through 439 Processing sheet with id=AH2, first strand: chain 'a' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER a 320 " --> pdb=" O SER a 327 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 334 through 338 removed outlier: 6.495A pdb=" N THR a 341 " --> pdb=" O THR a 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE a 423 " --> pdb=" O PRO a 402 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 436 through 439 Processing sheet with id=AH5, first strand: chain 'b' and resid 320 through 322 removed outlier: 6.384A pdb=" N SER b 320 " --> pdb=" O SER b 327 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'b' and resid 334 through 338 removed outlier: 6.496A pdb=" N THR b 341 " --> pdb=" O THR b 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE b 423 " --> pdb=" O PRO b 402 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'c' and resid 436 through 439 Processing sheet with id=AH8, first strand: chain 'c' and resid 320 through 322 removed outlier: 6.383A pdb=" N SER c 320 " --> pdb=" O SER c 327 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'c' and resid 334 through 338 removed outlier: 6.494A pdb=" N THR c 341 " --> pdb=" O THR c 337 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE c 423 " --> pdb=" O PRO c 402 " (cutoff:3.500A) 3080 hydrogen bonds defined for protein. 8778 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: 23.15 Time building geometry restraints manager: 20.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 8052 1.31 - 1.44: 11973 1.44 - 1.56: 26937 1.56 - 1.69: 14 1.69 - 1.81: 210 Bond restraints: 47186 Sorted by residual: bond pdb=" C ILE O 110 " pdb=" O ILE O 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.73e+01 bond pdb=" C ILE A 110 " pdb=" O ILE A 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.72e+01 bond pdb=" C ILE H 110 " pdb=" O ILE H 110 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.13e-02 7.83e+03 1.69e+01 bond pdb=" C ILE L 110 " pdb=" O ILE L 110 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.13e-02 7.83e+03 1.69e+01 bond pdb=" C ILE E 110 " pdb=" O ILE E 110 " ideal model delta sigma weight residual 1.237 1.190 0.046 1.13e-02 7.83e+03 1.69e+01 ... (remaining 47181 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.79: 1083 106.79 - 113.55: 25793 113.55 - 120.32: 17839 120.32 - 127.08: 18933 127.08 - 133.85: 224 Bond angle restraints: 63872 Sorted by residual: angle pdb=" N PRO K 4 " pdb=" CA PRO K 4 " pdb=" CB PRO K 4 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" N PRO J 4 " pdb=" CA PRO J 4 " pdb=" CB PRO J 4 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N GLY O 227 " pdb=" CA GLY O 227 " pdb=" C GLY O 227 " ideal model delta sigma weight residual 111.50 123.19 -11.69 1.74e+00 3.30e-01 4.51e+01 angle pdb=" N GLY M 227 " pdb=" CA GLY M 227 " pdb=" C GLY M 227 " ideal model delta sigma weight residual 111.50 123.18 -11.68 1.74e+00 3.30e-01 4.50e+01 angle pdb=" N GLY J 227 " pdb=" CA GLY J 227 " pdb=" C GLY J 227 " ideal model delta sigma weight residual 111.50 123.18 -11.68 1.74e+00 3.30e-01 4.50e+01 ... (remaining 63867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 26434 17.23 - 34.47: 1450 34.47 - 51.70: 340 51.70 - 68.93: 127 68.93 - 86.16: 56 Dihedral angle restraints: 28407 sinusoidal: 10807 harmonic: 17600 Sorted by residual: dihedral pdb=" CA THR R 321 " pdb=" C THR R 321 " pdb=" N GLN R 322 " pdb=" CA GLN R 322 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR W 321 " pdb=" C THR W 321 " pdb=" N GLN W 322 " pdb=" CA GLN W 322 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA THR b 321 " pdb=" C THR b 321 " pdb=" N GLN b 322 " pdb=" CA GLN b 322 " ideal model delta harmonic sigma weight residual 180.00 163.51 16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 28404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 6023 0.067 - 0.135: 1069 0.135 - 0.202: 144 0.202 - 0.269: 25 0.269 - 0.336: 14 Chirality restraints: 7275 Sorted by residual: chirality pdb=" CA GLN I 114 " pdb=" N GLN I 114 " pdb=" C GLN I 114 " pdb=" CB GLN I 114 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA GLN F 114 " pdb=" N GLN F 114 " pdb=" C GLN F 114 " pdb=" CB GLN F 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA GLN G 114 " pdb=" N GLN G 114 " pdb=" C GLN G 114 " pdb=" CB GLN G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 7272 not shown) Planarity restraints: 8424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " 0.096 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO L 9 " -0.260 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " 0.089 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 8 " -0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO A 9 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE J 111 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C PHE J 111 " -0.056 2.00e-02 2.50e+03 pdb=" O PHE J 111 " 0.021 2.00e-02 2.50e+03 pdb=" N THR J 112 " 0.019 2.00e-02 2.50e+03 ... (remaining 8421 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.98: 26 1.98 - 2.71: 1844 2.71 - 3.44: 65871 3.44 - 4.17: 104288 4.17 - 4.90: 190256 Nonbonded interactions: 362285 Sorted by model distance: nonbonded pdb=" NH2 ARG D 135 " pdb=" NH1 ARG E 48 " model vdw 1.245 3.200 nonbonded pdb=" NH2 ARG E 135 " pdb=" NH1 ARG F 48 " model vdw 1.289 3.200 nonbonded pdb=" O GLY I 66 " pdb=" O LEU h 174 " model vdw 1.410 3.040 nonbonded pdb=" O GLY F 66 " pdb=" O LEU e 174 " model vdw 1.429 3.040 nonbonded pdb=" NH2 ARG C 135 " pdb=" NH1 ARG D 48 " model vdw 1.485 3.200 ... (remaining 362280 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 8 through 234) selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and resid 8 through 234) selection = (chain 'K' and resid 8 through 234) selection = (chain 'L' and resid 8 through 234) selection = (chain 'M' and resid 8 through 234) selection = (chain 'N' and resid 8 through 234) selection = (chain 'O' and resid 8 through 234) } ncs_group { reference = (chain 'P' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Q' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'R' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'S' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = chain 'T' selection = (chain 'U' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'V' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'W' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'X' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Y' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'Z' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'a' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'b' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) selection = (chain 'c' and ((resid 301 and (name N or name CA or name C or name O or name CB \ )) or resid 302 through 522)) } ncs_group { reference = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.920 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: 0.040 Extract box with map and model: 18.190 Check model and map are aligned: 0.710 Set scattering table: 0.400 Process input model: 122.740 Find NCS groups from input model: 4.010 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.007 0.061 47186 Z= 0.454 Angle : 0.987 16.548 63872 Z= 0.614 Chirality : 0.054 0.336 7275 Planarity : 0.007 0.150 8424 Dihedral : 12.926 86.163 17201 Min Nonbonded Distance : 1.245 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer Outliers : 1.01 % 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: -0.26 (0.11), residues: 6072 helix: 0.80 (0.11), residues: 2541 sheet: -0.71 (0.12), residues: 1526 loop : -0.80 (0.14), residues: 2005 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 973 time to evaluate : 5.040 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 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 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 11 residues processed: 1008 average time/residue: 0.5968 time to fit residues: 955.8638 Evaluate side-chains 423 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 412 time to evaluate : 5.315 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 1.1311 time to fit residues: 23.1522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 307 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 471 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 546 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 105 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 98 GLN E 11 GLN F 11 GLN G 11 GLN H 11 GLN I 11 GLN J 11 GLN J 231 GLN K 11 GLN K 231 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 231 GLN M 11 GLN N 11 GLN O 11 GLN R 456 GLN S 456 GLN U 456 GLN V 456 GLN Y 456 GLN Z 390 ASN a 456 GLN b 456 GLN ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 456 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 47186 Z= 0.263 Angle : 0.626 7.544 63872 Z= 0.346 Chirality : 0.044 0.218 7275 Planarity : 0.005 0.075 8424 Dihedral : 4.563 79.020 6877 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.46 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.11), residues: 6072 helix: 2.07 (0.10), residues: 2583 sheet: 0.04 (0.13), residues: 1485 loop : -0.63 (0.13), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 522 time to evaluate : 5.155 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 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 524 average time/residue: 0.5661 time to fit residues: 494.7962 Evaluate side-chains 315 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 5.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 454 optimal weight: 0.9980 chunk 372 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 547 optimal weight: 7.9990 chunk 591 optimal weight: 8.9990 chunk 487 optimal weight: 7.9990 chunk 543 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 ASN F 165 ASN G 105 GLN H 114 GLN H 165 ASN J 114 GLN K 114 GLN L 11 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 231 GLN ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 415 GLN e 172 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 47186 Z= 0.266 Angle : 0.596 8.797 63872 Z= 0.329 Chirality : 0.042 0.163 7275 Planarity : 0.004 0.053 8424 Dihedral : 4.301 64.829 6877 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer Outliers : 0.09 % 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: 1.39 (0.11), residues: 6072 helix: 2.47 (0.10), residues: 2583 sheet: 0.42 (0.13), residues: 1482 loop : -0.75 (0.13), residues: 2007 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 403 time to evaluate : 5.217 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 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: 4 outliers final: 0 residues processed: 407 average time/residue: 0.5799 time to fit residues: 394.2975 Evaluate side-chains 258 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 5.356 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 6.9990 chunk 411 optimal weight: 1.9990 chunk 284 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 549 optimal weight: 6.9990 chunk 581 optimal weight: 5.9990 chunk 287 optimal weight: 20.0000 chunk 520 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN D 105 GLN E 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN H 114 GLN I 101 ASN L 105 GLN L 165 ASN ** O 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 396 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 47186 Z= 0.258 Angle : 0.570 8.377 63872 Z= 0.313 Chirality : 0.042 0.226 7275 Planarity : 0.004 0.047 8424 Dihedral : 4.281 67.766 6877 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.67 % Rotamer Outliers : 0.15 % 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: 1.53 (0.11), residues: 6072 helix: 2.63 (0.10), residues: 2592 sheet: 0.61 (0.13), residues: 1445 loop : -0.86 (0.13), residues: 2035 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 367 time to evaluate : 5.324 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 372 average time/residue: 0.5376 time to fit residues: 337.6807 Evaluate side-chains 239 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 5.037 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4715 time to fit residues: 7.2764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 6.9990 chunk 330 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 496 optimal weight: 0.0980 chunk 402 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 522 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN H 114 GLN L 105 GLN L 114 GLN L 165 ASN M 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 47186 Z= 0.135 Angle : 0.492 9.516 63872 Z= 0.269 Chirality : 0.041 0.184 7275 Planarity : 0.003 0.040 8424 Dihedral : 4.027 65.438 6877 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer Outliers : 0.09 % 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: 1.86 (0.11), residues: 6072 helix: 2.94 (0.10), residues: 2590 sheet: 0.82 (0.13), residues: 1425 loop : -0.74 (0.13), residues: 2057 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 376 time to evaluate : 5.480 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 378 average time/residue: 0.5682 time to fit residues: 363.0662 Evaluate side-chains 247 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 5.544 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 143 optimal weight: 20.0000 chunk 582 optimal weight: 7.9990 chunk 483 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN H 114 GLN J 165 ASN L 105 GLN L 165 ASN U 390 ASN Y 430 ASN Z 322 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.7680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 47186 Z= 0.289 Angle : 0.577 9.535 63872 Z= 0.316 Chirality : 0.042 0.152 7275 Planarity : 0.004 0.041 8424 Dihedral : 4.242 73.768 6877 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer Outliers : 0.09 % 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: 1.67 (0.11), residues: 6072 helix: 2.77 (0.10), residues: 2594 sheet: 0.77 (0.13), residues: 1412 loop : -0.87 (0.13), residues: 2066 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 315 time to evaluate : 5.139 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 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: 4 outliers final: 0 residues processed: 319 average time/residue: 0.5503 time to fit residues: 299.8902 Evaluate side-chains 226 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 5.427 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 331 optimal weight: 3.9990 chunk 425 optimal weight: 0.9980 chunk 329 optimal weight: 4.9990 chunk 490 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 580 optimal weight: 3.9990 chunk 363 optimal weight: 9.9990 chunk 353 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN H 231 GLN I 114 GLN L 105 GLN L 165 ASN U 390 ASN a 415 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.7820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 47186 Z= 0.166 Angle : 0.505 8.173 63872 Z= 0.277 Chirality : 0.041 0.272 7275 Planarity : 0.003 0.038 8424 Dihedral : 4.127 87.107 6877 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer Outliers : 0.09 % 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: 1.85 (0.11), residues: 6072 helix: 2.94 (0.10), residues: 2594 sheet: 0.87 (0.13), residues: 1402 loop : -0.82 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 343 time to evaluate : 5.533 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 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: 4 outliers final: 0 residues processed: 346 average time/residue: 0.5454 time to fit residues: 322.4639 Evaluate side-chains 233 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 5.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 346 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 368 optimal weight: 5.9990 chunk 395 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 456 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN I 114 GLN I 231 GLN L 105 GLN ** L 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN U 390 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 47186 Z= 0.292 Angle : 0.591 7.777 63872 Z= 0.324 Chirality : 0.042 0.254 7275 Planarity : 0.004 0.040 8424 Dihedral : 4.324 77.239 6877 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.02 % Favored : 95.95 % Rotamer Outliers : 0.09 % 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: 1.58 (0.11), residues: 6072 helix: 2.67 (0.10), residues: 2594 sheet: 0.84 (0.13), residues: 1392 loop : -0.97 (0.13), residues: 2086 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 309 time to evaluate : 5.221 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 312 average time/residue: 0.5587 time to fit residues: 296.1912 Evaluate side-chains 218 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 5.406 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.5949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 6.9990 chunk 555 optimal weight: 6.9990 chunk 507 optimal weight: 2.9990 chunk 540 optimal weight: 8.9990 chunk 325 optimal weight: 0.0370 chunk 235 optimal weight: 9.9990 chunk 424 optimal weight: 3.9990 chunk 165 optimal weight: 0.0370 chunk 488 optimal weight: 4.9990 chunk 511 optimal weight: 1.9990 chunk 538 optimal weight: 9.9990 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN L 105 GLN L 165 ASN ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 390 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.8224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.050 47186 Z= 0.156 Angle : 0.511 8.501 63872 Z= 0.279 Chirality : 0.042 0.220 7275 Planarity : 0.003 0.038 8424 Dihedral : 4.055 73.908 6877 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.78 % Favored : 97.18 % Rotamer Outliers : 0.09 % 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: 1.85 (0.11), residues: 6072 helix: 2.94 (0.10), residues: 2594 sheet: 0.86 (0.13), residues: 1426 loop : -0.83 (0.13), residues: 2052 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 5.579 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 331 average time/residue: 0.5585 time to fit residues: 315.3539 Evaluate side-chains 228 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 5.078 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 0.9990 chunk 571 optimal weight: 1.9990 chunk 348 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 397 optimal weight: 6.9990 chunk 599 optimal weight: 6.9990 chunk 551 optimal weight: 2.9990 chunk 477 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 368 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 GLN L 105 GLN ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 47186 Z= 0.160 Angle : 0.510 10.895 63872 Z= 0.278 Chirality : 0.042 0.202 7275 Planarity : 0.003 0.041 8424 Dihedral : 3.986 71.974 6877 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.41 % Favored : 96.56 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.11), residues: 6072 helix: 2.96 (0.10), residues: 2598 sheet: 0.99 (0.13), residues: 1405 loop : -0.81 (0.13), residues: 2069 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12144 Ramachandran restraints generated. 6072 Oldfield, 0 Emsley, 6072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 317 time to evaluate : 5.438 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 319 average time/residue: 0.5707 time to fit residues: 310.5641 Evaluate side-chains 227 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 5.391 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 3.9990 chunk 508 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 440 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 478 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 491 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN I 101 ASN L 105 GLN ** U 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.033129 restraints weight = 295429.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.034382 restraints weight = 181587.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.035279 restraints weight = 130163.399| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.8367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 47186 Z= 0.125 Angle : 0.495 10.113 63872 Z= 0.268 Chirality : 0.042 0.191 7275 Planarity : 0.003 0.042 8424 Dihedral : 3.889 83.406 6877 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.67 % Favored : 97.30 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.11), residues: 6072 helix: 3.02 (0.10), residues: 2602 sheet: 1.04 (0.14), residues: 1416 loop : -0.76 (0.13), residues: 2054 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8111.56 seconds wall clock time: 149 minutes 12.31 seconds (8952.31 seconds total)