Starting phenix.real_space_refine on Mon Mar 25 06:06:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/03_2024/6bgo_7098_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/03_2024/6bgo_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_7098/03_2024/6bgo_7098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/03_2024/6bgo_7098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/03_2024/6bgo_7098_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgo_7098/03_2024/6bgo_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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.14, per 1000 atoms: 0.48 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: 16.07 Conformation dependent library (CDL) restraints added in 7.5 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: 5.55 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: 20.38 Time building geometry restraints manager: 17.52 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: 5.250 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: 16.770 Check model and map are aligned: 0.330 Set scattering table: 0.370 Process input model: 113.500 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.300 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.130 ------------------------------------------------------------------------------- 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 % Allowed : 5.00 % Favored : 93.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP c 429 HIS 0.006 0.001 HIS P 365 PHE 0.030 0.004 PHE F 68 TYR 0.015 0.002 TYR F 139 ARG 0.004 0.001 ARG M 217 *********************** 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 : 5.056 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 REVERT: C 41 PHE cc_start: 0.7780 (m-80) cc_final: 0.7562 (m-80) REVERT: D 118 TYR cc_start: 0.7936 (m-10) cc_final: 0.7215 (m-80) REVERT: E 143 TYR cc_start: 0.6627 (p90) cc_final: 0.6418 (p90) REVERT: E 147 ILE cc_start: 0.6938 (pt) cc_final: 0.6564 (pt) REVERT: G 163 ILE cc_start: 0.7196 (mt) cc_final: 0.6920 (mt) REVERT: H 45 ASN cc_start: 0.6236 (t0) cc_final: 0.5918 (t0) REVERT: H 122 LEU cc_start: 0.8860 (mt) cc_final: 0.8410 (mp) REVERT: H 147 ILE cc_start: 0.7946 (pt) cc_final: 0.7431 (pt) REVERT: H 209 GLU cc_start: 0.5404 (tt0) cc_final: 0.5012 (tt0) REVERT: J 41 PHE cc_start: 0.8232 (m-80) cc_final: 0.8012 (m-80) REVERT: L 58 ASP cc_start: 0.8973 (m-30) cc_final: 0.8683 (t70) REVERT: M 118 TYR cc_start: 0.7993 (m-10) cc_final: 0.7789 (m-80) REVERT: M 163 ILE cc_start: 0.8134 (mt) cc_final: 0.7702 (mt) REVERT: N 52 LYS cc_start: 0.8747 (mttt) cc_final: 0.8529 (mtpt) REVERT: N 121 GLU cc_start: 0.8827 (tt0) cc_final: 0.8509 (tp30) REVERT: O 156 MET cc_start: 0.7996 (mtm) cc_final: 0.7107 (mtm) REVERT: Q 376 PHE cc_start: 0.7961 (t80) cc_final: 0.7516 (t80) REVERT: Q 432 GLU cc_start: 0.8325 (tp30) cc_final: 0.8050 (tm-30) REVERT: S 447 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8204 (ttmm) REVERT: S 450 MET cc_start: 0.7312 (mtm) cc_final: 0.7054 (mtm) REVERT: V 376 PHE cc_start: 0.7898 (t80) cc_final: 0.7564 (t80) REVERT: V 380 ILE cc_start: 0.9258 (mt) cc_final: 0.8968 (mt) REVERT: Z 308 TYR cc_start: 0.8262 (p90) cc_final: 0.7867 (p90) REVERT: Z 390 ASN cc_start: 0.8168 (t0) cc_final: 0.7936 (t0) REVERT: a 390 ASN cc_start: 0.7982 (t0) cc_final: 0.7545 (t0) REVERT: b 376 PHE cc_start: 0.8113 (t80) cc_final: 0.7853 (t80) REVERT: b 383 LEU cc_start: 0.9189 (tp) cc_final: 0.8892 (tp) outliers start: 47 outliers final: 11 residues processed: 1008 average time/residue: 0.5993 time to fit residues: 965.3581 Evaluate side-chains 431 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 420 time to evaluate : 5.372 ------------------------------------------------------------------------------- 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: 4.9990 chunk 456 optimal weight: 4.9990 chunk 253 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 471 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 chunk 351 optimal weight: 2.9990 chunk 546 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 105 GLN J 165 ASN J 231 GLN K 11 GLN K 231 GLN ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 231 GLN O 11 GLN R 456 GLN S 456 GLN U 456 GLN V 456 GLN Y 456 GLN a 456 GLN b 456 GLN ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 456 GLN e 172 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 47186 Z= 0.280 Angle : 0.657 9.277 63872 Z= 0.362 Chirality : 0.044 0.217 7275 Planarity : 0.005 0.074 8424 Dihedral : 4.704 82.408 6877 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 2.76 % Favored : 97.18 % 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: 0.87 (0.10), residues: 6072 helix: 1.89 (0.10), residues: 2583 sheet: -0.03 (0.13), residues: 1548 loop : -0.64 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 429 HIS 0.006 0.001 HIS N 129 PHE 0.037 0.003 PHE J 71 TYR 0.020 0.002 TYR J 57 ARG 0.008 0.001 ARG O 14 *********************** 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 516 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 513 time to evaluate : 5.109 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: A 118 TYR cc_start: 0.8669 (m-80) cc_final: 0.8252 (m-80) REVERT: D 149 ASP cc_start: 0.8827 (p0) cc_final: 0.8476 (p0) REVERT: E 118 TYR cc_start: 0.8090 (m-80) cc_final: 0.7849 (m-80) REVERT: G 57 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.8009 (t80) REVERT: H 163 ILE cc_start: 0.7558 (mt) cc_final: 0.7026 (mt) REVERT: I 83 ASP cc_start: 0.9281 (p0) cc_final: 0.8789 (m-30) REVERT: I 163 ILE cc_start: 0.7771 (mp) cc_final: 0.7496 (mp) REVERT: I 167 LEU cc_start: 0.9116 (mt) cc_final: 0.8909 (mt) REVERT: J 167 LEU cc_start: 0.9113 (mt) cc_final: 0.8886 (tp) REVERT: M 116 LYS cc_start: 0.8924 (mmpt) cc_final: 0.8670 (ttpp) REVERT: N 58 ASP cc_start: 0.9395 (p0) cc_final: 0.9103 (p0) REVERT: O 163 ILE cc_start: 0.8712 (mp) cc_final: 0.8505 (mp) REVERT: U 322 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8380 (tm-30) REVERT: U 325 MET cc_start: 0.8825 (mpp) cc_final: 0.8273 (mpp) REVERT: U 335 TYR cc_start: 0.8379 (m-80) cc_final: 0.8119 (m-80) REVERT: U 432 GLU cc_start: 0.8286 (mp0) cc_final: 0.7640 (tm-30) REVERT: X 390 ASN cc_start: 0.8080 (t0) cc_final: 0.7727 (t0) REVERT: X 447 LYS cc_start: 0.9162 (mtmt) cc_final: 0.8877 (ttmm) REVERT: Z 330 ASP cc_start: 0.8899 (p0) cc_final: 0.8400 (p0) REVERT: a 325 MET cc_start: 0.8598 (tmm) cc_final: 0.8112 (tmm) REVERT: a 390 ASN cc_start: 0.7979 (t0) cc_final: 0.7409 (t0) REVERT: b 390 ASN cc_start: 0.7928 (t0) cc_final: 0.7558 (t0) REVERT: c 335 TYR cc_start: 0.8541 (m-80) cc_final: 0.8327 (m-80) REVERT: c 383 LEU cc_start: 0.9243 (tp) cc_final: 0.9041 (tp) outliers start: 3 outliers final: 0 residues processed: 515 average time/residue: 0.5565 time to fit residues: 477.0303 Evaluate side-chains 323 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 322 time to evaluate : 4.748 ------------------------------------------------------------------------------- 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: 2.9990 chunk 454 optimal weight: 3.9990 chunk 372 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 547 optimal weight: 20.0000 chunk 591 optimal weight: 0.0370 chunk 487 optimal weight: 0.6980 chunk 543 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 439 optimal weight: 0.4980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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** H 114 GLN I 98 GLN K 114 GLN L 11 GLN L 105 GLN M 231 GLN Z 396 GLN c 415 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 47186 Z= 0.124 Angle : 0.485 10.174 63872 Z= 0.262 Chirality : 0.042 0.168 7275 Planarity : 0.003 0.052 8424 Dihedral : 3.947 65.547 6877 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.78 % Rotamer: Outliers : 0.15 % Allowed : 1.75 % Favored : 98.10 % 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: 1.82 (0.11), residues: 6072 helix: 2.82 (0.10), residues: 2590 sheet: 0.59 (0.13), residues: 1485 loop : -0.50 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP V 429 HIS 0.004 0.001 HIS Q 365 PHE 0.033 0.002 PHE K 71 TYR 0.018 0.001 TYR T 359 ARG 0.007 0.000 ARG N 21 *********************** 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 488 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 481 time to evaluate : 4.882 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: A 58 ASP cc_start: 0.8909 (p0) cc_final: 0.8675 (p0) REVERT: A 163 ILE cc_start: 0.8456 (mp) cc_final: 0.8080 (mm) REVERT: C 156 MET cc_start: 0.7679 (ttm) cc_final: 0.7429 (mmm) REVERT: D 58 ASP cc_start: 0.9250 (p0) cc_final: 0.8962 (p0) REVERT: D 149 ASP cc_start: 0.8815 (p0) cc_final: 0.8491 (p0) REVERT: E 83 ASP cc_start: 0.8385 (p0) cc_final: 0.7710 (m-30) REVERT: E 105 GLN cc_start: 0.9038 (tm-30) cc_final: 0.8832 (tm-30) REVERT: E 118 TYR cc_start: 0.8137 (m-80) cc_final: 0.7894 (m-80) REVERT: G 58 ASP cc_start: 0.8597 (p0) cc_final: 0.8326 (p0) REVERT: H 110 ILE cc_start: 0.9167 (pt) cc_final: 0.8807 (pt) REVERT: H 163 ILE cc_start: 0.7535 (mt) cc_final: 0.7028 (mt) REVERT: I 80 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8501 (tm-30) REVERT: I 83 ASP cc_start: 0.9076 (p0) cc_final: 0.8812 (p0) REVERT: I 163 ILE cc_start: 0.7671 (mp) cc_final: 0.7334 (mp) REVERT: J 24 ILE cc_start: 0.9086 (mm) cc_final: 0.8800 (pt) REVERT: K 163 ILE cc_start: 0.8369 (mm) cc_final: 0.7406 (mm) REVERT: N 58 ASP cc_start: 0.9423 (p0) cc_final: 0.9191 (p0) REVERT: O 58 ASP cc_start: 0.9186 (p0) cc_final: 0.8905 (p0) REVERT: Q 390 ASN cc_start: 0.7446 (p0) cc_final: 0.6909 (p0) REVERT: U 325 MET cc_start: 0.8841 (mpp) cc_final: 0.8402 (mpp) REVERT: U 335 TYR cc_start: 0.8349 (m-80) cc_final: 0.8105 (m-80) REVERT: U 432 GLU cc_start: 0.8157 (mp0) cc_final: 0.7502 (tm-30) REVERT: X 390 ASN cc_start: 0.7624 (t0) cc_final: 0.7416 (t0) REVERT: b 390 ASN cc_start: 0.7839 (t0) cc_final: 0.7123 (t0) REVERT: g 173 TYR cc_start: 0.4827 (m-10) cc_final: 0.4540 (m-80) outliers start: 7 outliers final: 1 residues processed: 486 average time/residue: 0.5634 time to fit residues: 458.0399 Evaluate side-chains 315 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 5.291 ------------------------------------------------------------------------------- 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: 0.1980 chunk 411 optimal weight: 7.9990 chunk 284 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 367 optimal weight: 0.8980 chunk 549 optimal weight: 0.9980 chunk 581 optimal weight: 8.9990 chunk 287 optimal weight: 8.9990 chunk 520 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** H 114 GLN L 101 ASN L 105 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 47186 Z= 0.120 Angle : 0.472 9.448 63872 Z= 0.255 Chirality : 0.041 0.256 7275 Planarity : 0.003 0.047 8424 Dihedral : 3.844 63.455 6877 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 0.09 % Allowed : 1.27 % Favored : 98.64 % 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: 2.11 (0.11), residues: 6072 helix: 3.04 (0.10), residues: 2592 sheet: 0.89 (0.13), residues: 1471 loop : -0.45 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP V 429 HIS 0.003 0.001 HIS a 365 PHE 0.031 0.002 PHE K 71 TYR 0.011 0.001 TYR N 118 ARG 0.006 0.000 ARG c 509 *********************** 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 438 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 434 time to evaluate : 5.586 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: A 163 ILE cc_start: 0.8537 (mp) cc_final: 0.8114 (mm) REVERT: C 156 MET cc_start: 0.7843 (ttm) cc_final: 0.7414 (mmm) REVERT: D 58 ASP cc_start: 0.9250 (p0) cc_final: 0.8906 (p0) REVERT: D 149 ASP cc_start: 0.8981 (p0) cc_final: 0.8527 (p0) REVERT: E 83 ASP cc_start: 0.8355 (p0) cc_final: 0.7668 (m-30) REVERT: E 105 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8840 (tm-30) REVERT: E 163 ILE cc_start: 0.7997 (mp) cc_final: 0.7598 (mm) REVERT: G 58 ASP cc_start: 0.8664 (p0) cc_final: 0.8438 (p0) REVERT: H 110 ILE cc_start: 0.9175 (pt) cc_final: 0.8851 (pt) REVERT: I 80 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8482 (tm-30) REVERT: I 83 ASP cc_start: 0.9040 (p0) cc_final: 0.8829 (p0) REVERT: I 163 ILE cc_start: 0.7638 (mp) cc_final: 0.7377 (mp) REVERT: J 24 ILE cc_start: 0.9037 (mm) cc_final: 0.8804 (pt) REVERT: J 167 LEU cc_start: 0.9085 (mt) cc_final: 0.8812 (tp) REVERT: K 163 ILE cc_start: 0.8435 (mm) cc_final: 0.7554 (mm) REVERT: L 167 LEU cc_start: 0.9202 (mt) cc_final: 0.8976 (mt) REVERT: N 58 ASP cc_start: 0.9438 (p0) cc_final: 0.9119 (p0) REVERT: O 58 ASP cc_start: 0.8807 (p0) cc_final: 0.8543 (p0) REVERT: O 163 ILE cc_start: 0.8663 (mp) cc_final: 0.8349 (mp) REVERT: U 325 MET cc_start: 0.8950 (mpp) cc_final: 0.8465 (mpp) REVERT: U 335 TYR cc_start: 0.8372 (m-80) cc_final: 0.8142 (m-80) REVERT: U 432 GLU cc_start: 0.8201 (mp0) cc_final: 0.7460 (tm-30) REVERT: V 325 MET cc_start: 0.8918 (mmm) cc_final: 0.8608 (mmp) REVERT: a 390 ASN cc_start: 0.8114 (t0) cc_final: 0.7802 (t0) REVERT: a 469 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8619 (mp0) REVERT: b 390 ASN cc_start: 0.7558 (t0) cc_final: 0.7134 (t0) outliers start: 4 outliers final: 0 residues processed: 436 average time/residue: 0.5395 time to fit residues: 396.8200 Evaluate side-chains 305 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 5.173 ------------------------------------------------------------------------------- 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: 10.0000 chunk 330 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 433 optimal weight: 6.9990 chunk 240 optimal weight: 0.0570 chunk 496 optimal weight: 0.9990 chunk 402 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 522 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 2.3504 ------------------------------------------------------------------------------- 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 F 165 ASN H 114 GLN H 165 ASN I 101 ASN K 174 ASN L 105 GLN L 114 GLN M 114 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 47186 Z= 0.185 Angle : 0.512 7.610 63872 Z= 0.279 Chirality : 0.041 0.209 7275 Planarity : 0.003 0.049 8424 Dihedral : 3.913 72.142 6877 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 0.09 % Allowed : 1.72 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.11), residues: 6072 helix: 3.07 (0.10), residues: 2585 sheet: 0.97 (0.13), residues: 1437 loop : -0.57 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP V 429 HIS 0.002 0.001 HIS N 152 PHE 0.047 0.002 PHE N 71 TYR 0.017 0.001 TYR N 118 ARG 0.005 0.000 ARG a 388 *********************** 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 390 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 386 time to evaluate : 5.467 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: A 163 ILE cc_start: 0.8721 (mp) cc_final: 0.8328 (mm) REVERT: D 114 GLN cc_start: 0.6725 (tm-30) cc_final: 0.6478 (tm-30) REVERT: E 83 ASP cc_start: 0.8506 (p0) cc_final: 0.7813 (m-30) REVERT: E 163 ILE cc_start: 0.8213 (mp) cc_final: 0.7855 (mm) REVERT: H 110 ILE cc_start: 0.9201 (pt) cc_final: 0.8851 (pt) REVERT: I 80 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8560 (tm-30) REVERT: I 83 ASP cc_start: 0.9140 (p0) cc_final: 0.8914 (p0) REVERT: I 101 ASN cc_start: 0.9037 (m110) cc_final: 0.8763 (t0) REVERT: N 58 ASP cc_start: 0.9491 (p0) cc_final: 0.9261 (p0) REVERT: O 58 ASP cc_start: 0.9177 (p0) cc_final: 0.8922 (p0) REVERT: T 314 MET cc_start: 0.7791 (ttm) cc_final: 0.7574 (ttm) REVERT: U 325 MET cc_start: 0.9066 (mpp) cc_final: 0.8749 (mpp) REVERT: U 335 TYR cc_start: 0.8421 (m-80) cc_final: 0.8207 (m-80) REVERT: V 325 MET cc_start: 0.8909 (mmm) cc_final: 0.8600 (mmp) REVERT: W 395 MET cc_start: 0.8379 (ppp) cc_final: 0.8080 (ppp) REVERT: b 390 ASN cc_start: 0.8204 (t0) cc_final: 0.7628 (t0) outliers start: 4 outliers final: 0 residues processed: 390 average time/residue: 0.5455 time to fit residues: 359.9462 Evaluate side-chains 269 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 5.318 ------------------------------------------------------------------------------- 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: 8.9990 chunk 524 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 582 optimal weight: 4.9990 chunk 483 optimal weight: 7.9990 chunk 269 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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** L 105 GLN U 390 ASN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 47186 Z= 0.238 Angle : 0.561 7.529 63872 Z= 0.307 Chirality : 0.041 0.177 7275 Planarity : 0.004 0.039 8424 Dihedral : 4.178 76.358 6877 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.54 % Rotamer: Outliers : 0.09 % Allowed : 1.94 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.11), residues: 6072 helix: 2.91 (0.10), residues: 2565 sheet: 0.95 (0.13), residues: 1404 loop : -0.67 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP V 429 HIS 0.003 0.001 HIS J 152 PHE 0.050 0.002 PHE N 71 TYR 0.024 0.001 TYR N 118 ARG 0.012 0.000 ARG O 14 *********************** 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 361 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 357 time to evaluate : 5.267 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: D 58 ASP cc_start: 0.9083 (p0) cc_final: 0.8831 (p0) REVERT: D 114 GLN cc_start: 0.7428 (tm-30) cc_final: 0.6907 (tm-30) REVERT: E 83 ASP cc_start: 0.8604 (p0) cc_final: 0.7850 (m-30) REVERT: E 118 TYR cc_start: 0.8358 (m-80) cc_final: 0.7937 (m-80) REVERT: G 105 GLN cc_start: 0.9214 (tm-30) cc_final: 0.9003 (tm-30) REVERT: H 110 ILE cc_start: 0.9319 (pt) cc_final: 0.8769 (pt) REVERT: H 163 ILE cc_start: 0.8606 (mm) cc_final: 0.8401 (mm) REVERT: I 80 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8594 (tm-30) REVERT: I 83 ASP cc_start: 0.9164 (p0) cc_final: 0.8902 (p0) REVERT: J 163 ILE cc_start: 0.7677 (mp) cc_final: 0.7427 (mm) REVERT: K 80 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8191 (tp-100) REVERT: M 163 ILE cc_start: 0.8019 (mp) cc_final: 0.7338 (mm) REVERT: U 325 MET cc_start: 0.9166 (mpp) cc_final: 0.8948 (mpp) REVERT: V 325 MET cc_start: 0.8931 (mmm) cc_final: 0.8620 (mmp) REVERT: W 395 MET cc_start: 0.8315 (ppp) cc_final: 0.8033 (ppp) REVERT: b 395 MET cc_start: 0.8392 (pmm) cc_final: 0.8075 (pmm) REVERT: c 335 TYR cc_start: 0.8359 (m-80) cc_final: 0.8142 (m-10) outliers start: 4 outliers final: 0 residues processed: 360 average time/residue: 0.5505 time to fit residues: 335.3714 Evaluate side-chains 243 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 4.757 ------------------------------------------------------------------------------- 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: 4.9990 chunk 65 optimal weight: 6.9990 chunk 331 optimal weight: 9.9990 chunk 425 optimal weight: 3.9990 chunk 329 optimal weight: 5.9990 chunk 490 optimal weight: 8.9990 chunk 325 optimal weight: 0.4980 chunk 580 optimal weight: 3.9990 chunk 363 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 267 optimal weight: 0.2980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 GLN O 114 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.7534 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= 0.199 Angle : 0.523 8.443 63872 Z= 0.286 Chirality : 0.041 0.156 7275 Planarity : 0.003 0.037 8424 Dihedral : 4.083 78.986 6877 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 0.06 % Allowed : 1.21 % Favored : 98.73 % 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: 1.89 (0.11), residues: 6072 helix: 2.85 (0.10), residues: 2592 sheet: 1.02 (0.13), residues: 1421 loop : -0.73 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP V 429 HIS 0.002 0.001 HIS N 152 PHE 0.039 0.002 PHE N 71 TYR 0.018 0.001 TYR F 57 ARG 0.006 0.000 ARG O 14 *********************** 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 338 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 335 time to evaluate : 5.277 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: A 163 ILE cc_start: 0.8779 (mp) cc_final: 0.8329 (mm) REVERT: D 58 ASP cc_start: 0.9223 (p0) cc_final: 0.8948 (p0) REVERT: D 98 GLN cc_start: 0.8843 (pt0) cc_final: 0.8615 (pt0) REVERT: D 114 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6972 (tm-30) REVERT: E 83 ASP cc_start: 0.8663 (p0) cc_final: 0.7844 (m-30) REVERT: E 118 TYR cc_start: 0.8348 (m-80) cc_final: 0.7990 (m-80) REVERT: H 110 ILE cc_start: 0.9360 (pt) cc_final: 0.9099 (pt) REVERT: H 163 ILE cc_start: 0.8660 (mm) cc_final: 0.8434 (mm) REVERT: I 83 ASP cc_start: 0.9131 (p0) cc_final: 0.8898 (p0) REVERT: I 101 ASN cc_start: 0.9110 (m110) cc_final: 0.8782 (t0) REVERT: L 105 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8404 (tm-30) REVERT: L 156 MET cc_start: 0.8372 (tpp) cc_final: 0.8000 (tpp) REVERT: M 163 ILE cc_start: 0.8181 (mp) cc_final: 0.7510 (mm) REVERT: O 58 ASP cc_start: 0.9129 (p0) cc_final: 0.8901 (p0) REVERT: Q 390 ASN cc_start: 0.7754 (p0) cc_final: 0.7478 (p0) REVERT: V 325 MET cc_start: 0.8897 (mmm) cc_final: 0.8583 (mmp) REVERT: W 330 ASP cc_start: 0.8903 (p0) cc_final: 0.8558 (p0) REVERT: W 395 MET cc_start: 0.8241 (ppp) cc_final: 0.7989 (ppp) REVERT: Z 330 ASP cc_start: 0.9003 (p0) cc_final: 0.8758 (p0) outliers start: 3 outliers final: 0 residues processed: 338 average time/residue: 0.5468 time to fit residues: 315.6174 Evaluate side-chains 239 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 5.545 ------------------------------------------------------------------------------- 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: 2.9990 chunk 346 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 368 optimal weight: 0.9980 chunk 395 optimal weight: 7.9990 chunk 286 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 456 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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** J 114 GLN L 105 GLN O 114 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 47186 Z= 0.149 Angle : 0.497 7.777 63872 Z= 0.269 Chirality : 0.041 0.268 7275 Planarity : 0.003 0.037 8424 Dihedral : 3.968 80.471 6877 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 0.06 % Allowed : 0.80 % Favored : 99.14 % 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: 2.97 (0.10), residues: 2596 sheet: 1.04 (0.13), residues: 1428 loop : -0.68 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 429 HIS 0.001 0.000 HIS O 152 PHE 0.041 0.002 PHE N 71 TYR 0.023 0.001 TYR O 57 ARG 0.006 0.000 ARG O 14 *********************** 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 348 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 345 time to evaluate : 4.868 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: A 163 ILE cc_start: 0.8770 (mp) cc_final: 0.8337 (mm) REVERT: D 58 ASP cc_start: 0.9226 (p0) cc_final: 0.8902 (p0) REVERT: D 98 GLN cc_start: 0.8834 (pt0) cc_final: 0.8568 (pt0) REVERT: D 114 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6893 (tm-30) REVERT: G 58 ASP cc_start: 0.8617 (p0) cc_final: 0.8408 (p0) REVERT: I 80 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8584 (tm-30) REVERT: I 101 ASN cc_start: 0.9106 (m110) cc_final: 0.8773 (t0) REVERT: I 114 GLN cc_start: 0.7283 (tm-30) cc_final: 0.6908 (tm-30) REVERT: J 58 ASP cc_start: 0.8735 (p0) cc_final: 0.8433 (p0) REVERT: L 156 MET cc_start: 0.8479 (tpp) cc_final: 0.8116 (tpp) REVERT: M 105 GLN cc_start: 0.9244 (tm-30) cc_final: 0.9023 (tm-30) REVERT: O 58 ASP cc_start: 0.9031 (p0) cc_final: 0.8758 (p0) REVERT: O 83 ASP cc_start: 0.8312 (p0) cc_final: 0.8097 (p0) REVERT: U 432 GLU cc_start: 0.8229 (mp0) cc_final: 0.7443 (tm-30) REVERT: V 325 MET cc_start: 0.8827 (mmm) cc_final: 0.8555 (mmm) REVERT: W 330 ASP cc_start: 0.8877 (p0) cc_final: 0.8533 (p0) REVERT: Z 330 ASP cc_start: 0.8921 (p0) cc_final: 0.8674 (p0) REVERT: a 325 MET cc_start: 0.8711 (tmm) cc_final: 0.8476 (tmm) REVERT: b 396 GLN cc_start: 0.8326 (mp10) cc_final: 0.8031 (tm-30) REVERT: g 173 TYR cc_start: 0.6613 (m-80) cc_final: 0.6285 (m-80) outliers start: 3 outliers final: 0 residues processed: 347 average time/residue: 0.5405 time to fit residues: 320.6606 Evaluate side-chains 240 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 5.369 ------------------------------------------------------------------------------- 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: 9.9990 chunk 555 optimal weight: 10.0000 chunk 507 optimal weight: 8.9990 chunk 540 optimal weight: 9.9990 chunk 325 optimal weight: 1.9990 chunk 235 optimal weight: 8.9990 chunk 424 optimal weight: 0.9980 chunk 165 optimal weight: 0.0070 chunk 488 optimal weight: 7.9990 chunk 511 optimal weight: 2.9990 chunk 538 optimal weight: 0.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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** ** H 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 GLN M 114 GLN O 114 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 47186 Z= 0.133 Angle : 0.488 9.403 63872 Z= 0.263 Chirality : 0.041 0.225 7275 Planarity : 0.003 0.036 8424 Dihedral : 3.908 87.838 6877 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 0.06 % Allowed : 0.50 % Favored : 99.44 % 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: 2.09 (0.11), residues: 6072 helix: 3.04 (0.10), residues: 2596 sheet: 1.12 (0.13), residues: 1428 loop : -0.67 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP R 429 HIS 0.002 0.000 HIS a 365 PHE 0.039 0.002 PHE N 71 TYR 0.013 0.001 TYR O 57 ARG 0.007 0.000 ARG O 14 *********************** 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 346 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 343 time to evaluate : 5.140 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: A 163 ILE cc_start: 0.8856 (mp) cc_final: 0.8417 (mm) REVERT: D 58 ASP cc_start: 0.9221 (p0) cc_final: 0.8953 (p0) REVERT: D 98 GLN cc_start: 0.8805 (pt0) cc_final: 0.8542 (pt0) REVERT: D 149 ASP cc_start: 0.8757 (p0) cc_final: 0.8509 (p0) REVERT: E 83 ASP cc_start: 0.8539 (p0) cc_final: 0.8311 (p0) REVERT: G 58 ASP cc_start: 0.8610 (p0) cc_final: 0.8405 (p0) REVERT: G 105 GLN cc_start: 0.9233 (tm-30) cc_final: 0.9004 (tm-30) REVERT: I 80 GLN cc_start: 0.8780 (tm-30) cc_final: 0.8563 (tm-30) REVERT: I 83 ASP cc_start: 0.9020 (p0) cc_final: 0.8681 (m-30) REVERT: I 101 ASN cc_start: 0.9085 (m110) cc_final: 0.8751 (t0) REVERT: I 163 ILE cc_start: 0.9012 (mp) cc_final: 0.8721 (mm) REVERT: J 58 ASP cc_start: 0.8758 (p0) cc_final: 0.8449 (p0) REVERT: L 114 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8196 (tp-100) REVERT: L 156 MET cc_start: 0.8468 (tpp) cc_final: 0.8111 (tpp) REVERT: N 58 ASP cc_start: 0.9450 (p0) cc_final: 0.9221 (p0) REVERT: O 58 ASP cc_start: 0.8986 (p0) cc_final: 0.8696 (p0) REVERT: O 83 ASP cc_start: 0.8246 (p0) cc_final: 0.8007 (p0) REVERT: O 156 MET cc_start: 0.7889 (mmm) cc_final: 0.7477 (mmm) REVERT: U 432 GLU cc_start: 0.8119 (mp0) cc_final: 0.7408 (tm-30) REVERT: V 325 MET cc_start: 0.8765 (mmm) cc_final: 0.8505 (mmm) REVERT: W 330 ASP cc_start: 0.8852 (p0) cc_final: 0.8525 (p0) REVERT: Z 330 ASP cc_start: 0.8894 (p0) cc_final: 0.8638 (p0) REVERT: a 325 MET cc_start: 0.8684 (tmm) cc_final: 0.8454 (tmm) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.5556 time to fit residues: 323.3748 Evaluate side-chains 241 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 5.202 ------------------------------------------------------------------------------- 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: 9.9990 chunk 571 optimal weight: 9.9990 chunk 348 optimal weight: 6.9990 chunk 271 optimal weight: 0.4980 chunk 397 optimal weight: 5.9990 chunk 599 optimal weight: 5.9990 chunk 551 optimal weight: 2.9990 chunk 477 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 368 optimal weight: 0.9990 chunk 292 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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** L 105 GLN ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47186 Z= 0.159 Angle : 0.501 9.141 63872 Z= 0.272 Chirality : 0.041 0.225 7275 Planarity : 0.003 0.041 8424 Dihedral : 3.923 89.445 6877 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.11), residues: 6072 helix: 3.04 (0.10), residues: 2596 sheet: 1.19 (0.13), residues: 1407 loop : -0.72 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 429 HIS 0.002 0.000 HIS N 152 PHE 0.041 0.002 PHE N 71 TYR 0.013 0.001 TYR O 57 ARG 0.009 0.000 ARG K 97 ********************** 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 329 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 326 time to evaluate : 5.229 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: A 156 MET cc_start: 0.6782 (mmm) cc_final: 0.6541 (mmm) REVERT: A 163 ILE cc_start: 0.8889 (mp) cc_final: 0.8468 (mm) REVERT: D 58 ASP cc_start: 0.9266 (p0) cc_final: 0.9035 (p0) REVERT: D 98 GLN cc_start: 0.8812 (pt0) cc_final: 0.8539 (pt0) REVERT: D 114 GLN cc_start: 0.6633 (tm-30) cc_final: 0.6174 (tm-30) REVERT: D 149 ASP cc_start: 0.8678 (p0) cc_final: 0.8452 (p0) REVERT: G 58 ASP cc_start: 0.8610 (p0) cc_final: 0.8395 (p0) REVERT: I 101 ASN cc_start: 0.9111 (m110) cc_final: 0.8776 (t0) REVERT: I 163 ILE cc_start: 0.9103 (mp) cc_final: 0.8815 (mm) REVERT: J 58 ASP cc_start: 0.8779 (p0) cc_final: 0.8463 (p0) REVERT: L 114 GLN cc_start: 0.8457 (tp-100) cc_final: 0.8009 (tp40) REVERT: L 156 MET cc_start: 0.8437 (tpp) cc_final: 0.8078 (tpp) REVERT: O 58 ASP cc_start: 0.9025 (p0) cc_final: 0.8795 (p0) REVERT: O 83 ASP cc_start: 0.8231 (p0) cc_final: 0.7994 (p0) REVERT: O 156 MET cc_start: 0.7869 (mmm) cc_final: 0.7633 (mmm) REVERT: U 432 GLU cc_start: 0.8134 (mp0) cc_final: 0.7440 (tm-30) REVERT: V 325 MET cc_start: 0.8761 (mmm) cc_final: 0.8498 (mmm) REVERT: W 330 ASP cc_start: 0.8858 (p0) cc_final: 0.8543 (p0) REVERT: X 500 ASP cc_start: 0.9356 (m-30) cc_final: 0.9126 (p0) REVERT: Z 330 ASP cc_start: 0.8924 (p0) cc_final: 0.8656 (p0) REVERT: a 325 MET cc_start: 0.8625 (tmm) cc_final: 0.8384 (tmm) REVERT: j 174 LEU cc_start: 0.8176 (mt) cc_final: 0.7968 (mt) outliers start: 3 outliers final: 0 residues processed: 328 average time/residue: 0.5219 time to fit residues: 291.1088 Evaluate side-chains 237 residues out of total 4665 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 4.508 ------------------------------------------------------------------------------- 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: 6.9990 chunk 508 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 440 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 478 optimal weight: 7.9990 chunk 200 optimal weight: 0.0770 chunk 491 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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** F 114 GLN L 105 GLN O 114 GLN ** V 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 322 GLN ** e 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.043370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.032845 restraints weight = 300307.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.034094 restraints weight = 183697.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.034929 restraints weight = 131194.461| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.8111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 47186 Z= 0.165 Angle : 0.503 8.591 63872 Z= 0.273 Chirality : 0.041 0.211 7275 Planarity : 0.003 0.040 8424 Dihedral : 3.937 88.651 6877 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 0.06 % Allowed : 0.11 % Favored : 99.83 % 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: 2.10 (0.11), residues: 6072 helix: 3.05 (0.10), residues: 2596 sheet: 1.19 (0.13), residues: 1407 loop : -0.71 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP V 429 HIS 0.001 0.000 HIS O 152 PHE 0.040 0.002 PHE N 71 TYR 0.015 0.001 TYR F 103 ARG 0.008 0.000 ARG K 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8503.86 seconds wall clock time: 155 minutes 5.94 seconds (9305.94 seconds total)