Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 17 09:44:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/07_2023/6c9k_7437.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 108 5.16 5 C 23733 2.51 5 N 6510 2.21 5 O 7281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 37632 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 1 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "I" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 1 Chain: "J" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "K" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "L" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "Q" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain: "R" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "S" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "T" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 17.24, per 1000 atoms: 0.46 Number of scatterers: 37632 At special positions: 0 Unit cell: (191.915, 195.19, 161.13, 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 108 16.00 O 7281 8.00 N 6510 7.00 C 23733 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: 14.08 Conformation dependent library (CDL) restraints added in 5.6 seconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 24 sheets defined 62.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.531A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.552A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 175 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'B' and resid 24 through 45 Processing helix chain 'B' and resid 49 through 72 Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.725A pdb=" N GLU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 137 removed outlier: 3.543A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 175 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.601A pdb=" N ARG B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 49 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.688A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 137 removed outlier: 3.504A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 175 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 265 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 80 through 96 removed outlier: 4.059A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 137 Processing helix chain 'D' and resid 139 through 175 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 232 through 240 Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'G' and resid 17 through 31 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 73 through 91 Processing helix chain 'I' and resid 24 through 45 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.530A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 137 removed outlier: 3.569A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 175 Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 208 Processing helix chain 'I' and resid 209 through 219 Processing helix chain 'I' and resid 232 through 240 Processing helix chain 'I' and resid 242 through 252 Processing helix chain 'I' and resid 265 through 273 Processing helix chain 'I' and resid 275 through 285 Processing helix chain 'I' and resid 298 through 306 Processing helix chain 'I' and resid 308 through 315 Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 49 through 72 Processing helix chain 'J' and resid 80 through 96 removed outlier: 4.174A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 137 Processing helix chain 'J' and resid 139 through 175 Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 208 Processing helix chain 'J' and resid 209 through 219 Processing helix chain 'J' and resid 232 through 240 Processing helix chain 'J' and resid 242 through 252 Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'J' and resid 275 through 285 Processing helix chain 'J' and resid 298 through 306 Processing helix chain 'J' and resid 308 through 315 Processing helix chain 'K' and resid 24 through 45 Processing helix chain 'K' and resid 49 through 72 Processing helix chain 'K' and resid 80 through 96 removed outlier: 3.560A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 137 Processing helix chain 'K' and resid 139 through 175 Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 208 Processing helix chain 'K' and resid 209 through 219 Processing helix chain 'K' and resid 232 through 240 Processing helix chain 'K' and resid 242 through 252 Processing helix chain 'K' and resid 265 through 273 Processing helix chain 'K' and resid 275 through 285 Processing helix chain 'K' and resid 298 through 306 Processing helix chain 'K' and resid 308 through 315 Processing helix chain 'L' and resid 24 through 45 Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 80 through 96 removed outlier: 4.030A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 removed outlier: 3.548A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 175 Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 208 Processing helix chain 'L' and resid 209 through 219 Processing helix chain 'L' and resid 232 through 240 Processing helix chain 'L' and resid 242 through 252 Processing helix chain 'L' and resid 265 through 273 Processing helix chain 'L' and resid 275 through 285 Processing helix chain 'L' and resid 298 through 306 Processing helix chain 'L' and resid 308 through 315 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 36 through 39 Processing helix chain 'M' and resid 73 through 91 Processing helix chain 'N' and resid 17 through 31 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 73 through 91 Processing helix chain 'O' and resid 17 through 31 Processing helix chain 'O' and resid 36 through 39 Processing helix chain 'O' and resid 73 through 91 Processing helix chain 'P' and resid 17 through 31 Processing helix chain 'P' and resid 36 through 39 Processing helix chain 'P' and resid 73 through 91 Processing helix chain 'Q' and resid 24 through 45 Processing helix chain 'Q' and resid 49 through 72 Processing helix chain 'Q' and resid 80 through 96 removed outlier: 3.553A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 137 removed outlier: 3.549A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 175 Processing helix chain 'Q' and resid 176 through 186 Processing helix chain 'Q' and resid 199 through 208 Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 232 through 240 Processing helix chain 'Q' and resid 242 through 252 Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 275 through 285 Processing helix chain 'Q' and resid 298 through 306 Processing helix chain 'Q' and resid 308 through 315 Processing helix chain 'R' and resid 24 through 45 Processing helix chain 'R' and resid 46 through 48 No H-bonds generated for 'chain 'R' and resid 46 through 48' Processing helix chain 'R' and resid 49 through 72 Processing helix chain 'R' and resid 80 through 97 removed outlier: 4.117A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 137 removed outlier: 3.507A pdb=" N LYS R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 175 Processing helix chain 'R' and resid 176 through 186 Processing helix chain 'R' and resid 199 through 208 Processing helix chain 'R' and resid 209 through 219 Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 265 through 273 Processing helix chain 'R' and resid 275 through 285 Processing helix chain 'R' and resid 298 through 306 Processing helix chain 'R' and resid 308 through 315 Processing helix chain 'S' and resid 24 through 45 Processing helix chain 'S' and resid 49 through 72 Processing helix chain 'S' and resid 80 through 96 removed outlier: 3.681A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 removed outlier: 3.532A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 175 Processing helix chain 'S' and resid 176 through 186 Processing helix chain 'S' and resid 199 through 208 Processing helix chain 'S' and resid 209 through 219 Processing helix chain 'S' and resid 232 through 240 Processing helix chain 'S' and resid 242 through 252 Processing helix chain 'S' and resid 265 through 273 Processing helix chain 'S' and resid 275 through 285 Processing helix chain 'S' and resid 298 through 306 Processing helix chain 'S' and resid 308 through 315 Processing helix chain 'T' and resid 24 through 45 Processing helix chain 'T' and resid 49 through 72 Processing helix chain 'T' and resid 80 through 96 removed outlier: 4.132A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 137 Processing helix chain 'T' and resid 139 through 175 Processing helix chain 'T' and resid 176 through 186 Processing helix chain 'T' and resid 199 through 208 Processing helix chain 'T' and resid 209 through 219 Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 242 through 252 Processing helix chain 'T' and resid 265 through 273 Processing helix chain 'T' and resid 275 through 285 Processing helix chain 'T' and resid 298 through 306 Processing helix chain 'T' and resid 308 through 315 Processing helix chain 'U' and resid 17 through 31 Processing helix chain 'U' and resid 36 through 39 Processing helix chain 'U' and resid 73 through 91 Processing helix chain 'V' and resid 17 through 31 Processing helix chain 'V' and resid 36 through 39 Processing helix chain 'V' and resid 73 through 91 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 36 through 39 Processing helix chain 'W' and resid 73 through 91 Processing helix chain 'X' and resid 17 through 31 Processing helix chain 'X' and resid 36 through 39 Processing helix chain 'X' and resid 73 through 91 Processing sheet with id=AA1, first strand: chain 'M' and resid 50 through 52 removed outlier: 6.548A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 62 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU E 105 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA E 64 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG E 107 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 66 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET E 109 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE E 68 " --> pdb=" O MET E 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.637A pdb=" N ARG E 13 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 52 removed outlier: 6.591A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.640A pdb=" N LEU M 62 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU M 105 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 64 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG M 107 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU M 66 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET M 109 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE M 68 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 50 through 52 removed outlier: 6.501A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 62 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU F 105 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA F 64 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG F 107 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU F 66 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET F 109 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE F 68 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'F' and resid 50 through 52 removed outlier: 6.593A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.015A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 removed outlier: 6.627A pdb=" N ARG G 13 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 50 through 52 removed outlier: 6.538A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU H 62 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU H 105 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA H 64 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG H 107 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU H 66 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET H 109 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE H 68 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.451A pdb=" N ARG H 13 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 50 through 52 removed outlier: 6.520A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU W 62 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU W 105 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA W 64 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG W 107 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU W 66 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET W 109 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE W 68 " --> pdb=" O MET W 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.987A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=AB6, first strand: chain 'O' and resid 50 through 52 removed outlier: 6.490A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 50 through 52 removed outlier: 6.596A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU X 62 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLU X 105 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA X 64 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG X 107 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 66 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET X 109 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE X 68 " --> pdb=" O MET X 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.571A pdb=" N LEU O 62 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLU O 105 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA O 64 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG O 107 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU O 66 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET O 109 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE O 68 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 removed outlier: 6.522A pdb=" N ARG O 13 " --> pdb=" O ALA O 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 removed outlier: 6.446A pdb=" N ARG P 13 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.556A pdb=" N ARG W 13 " --> pdb=" O ALA W 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.429A pdb=" N ARG X 13 " --> pdb=" O ALA X 93 " (cutoff:3.500A) 2475 hydrogen bonds defined for protein. 7269 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: 12.54 Time building geometry restraints manager: 15.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 36161 1.54 - 1.90: 1963 1.90 - 2.26: 0 2.26 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 38125 Sorted by residual: bond pdb=" C LEU Q 100 " pdb=" N SER Q 102 " ideal model delta sigma weight residual 1.330 2.991 -1.660 1.30e-02 5.92e+03 1.63e+04 bond pdb=" C GLU B 163 " pdb=" N LEU B 164 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.38e-02 5.25e+03 2.63e+02 bond pdb=" C GLU R 163 " pdb=" N LEU R 164 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.38e-02 5.25e+03 2.63e+02 bond pdb=" C GLU J 163 " pdb=" N LEU J 164 " ideal model delta sigma weight residual 1.335 1.558 -0.223 1.38e-02 5.25e+03 2.62e+02 bond pdb=" C GLU D 163 " pdb=" N LEU D 164 " ideal model delta sigma weight residual 1.335 1.544 -0.209 1.34e-02 5.57e+03 2.44e+02 ... (remaining 38120 not shown) Histogram of bond angle deviations from ideal: 95.68 - 103.34: 229 103.34 - 110.99: 15134 110.99 - 118.65: 16620 118.65 - 126.30: 19205 126.30 - 133.96: 358 Bond angle restraints: 51546 Sorted by residual: angle pdb=" CA LEU Q 100 " pdb=" C LEU Q 100 " pdb=" N SER Q 102 " ideal model delta sigma weight residual 115.51 95.68 19.83 1.27e+00 6.20e-01 2.44e+02 angle pdb=" C GLU S 163 " pdb=" N LEU S 164 " pdb=" CA LEU S 164 " ideal model delta sigma weight residual 120.31 108.19 12.12 1.52e+00 4.33e-01 6.36e+01 angle pdb=" C GLU C 163 " pdb=" N LEU C 164 " pdb=" CA LEU C 164 " ideal model delta sigma weight residual 120.31 108.25 12.06 1.52e+00 4.33e-01 6.29e+01 angle pdb=" C GLU K 163 " pdb=" N LEU K 164 " pdb=" CA LEU K 164 " ideal model delta sigma weight residual 120.31 108.27 12.04 1.52e+00 4.33e-01 6.28e+01 angle pdb=" C GLU Q 163 " pdb=" N LEU Q 164 " pdb=" CA LEU Q 164 " ideal model delta sigma weight residual 120.31 109.40 10.91 1.52e+00 4.33e-01 5.15e+01 ... (remaining 51541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 22117 17.70 - 35.39: 580 35.39 - 53.09: 149 53.09 - 70.78: 125 70.78 - 88.48: 31 Dihedral angle restraints: 23002 sinusoidal: 9000 harmonic: 14002 Sorted by residual: dihedral pdb=" CA LEU Q 100 " pdb=" C LEU Q 100 " pdb=" N SER Q 102 " pdb=" CA SER Q 102 " ideal model delta harmonic sigma weight residual 180.00 110.32 69.68 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA ASP U 70 " pdb=" CB ASP U 70 " pdb=" CG ASP U 70 " pdb=" OD1 ASP U 70 " ideal model delta sinusoidal sigma weight residual -30.00 -87.07 57.07 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP W 70 " pdb=" CB ASP W 70 " pdb=" CG ASP W 70 " pdb=" OD1 ASP W 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.94 56.94 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 22999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4307 0.067 - 0.134: 1429 0.134 - 0.201: 269 0.201 - 0.268: 32 0.268 - 0.335: 23 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA HIS T 202 " pdb=" N HIS T 202 " pdb=" C HIS T 202 " pdb=" CB HIS T 202 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA HIS B 202 " pdb=" N HIS B 202 " pdb=" C HIS B 202 " pdb=" CB HIS B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA HIS K 202 " pdb=" N HIS K 202 " pdb=" C HIS K 202 " pdb=" CB HIS K 202 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 6057 not shown) Planarity restraints: 6688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 100 " 0.078 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C LEU Q 100 " -0.257 2.00e-02 2.50e+03 pdb=" O LEU Q 100 " 0.137 2.00e-02 2.50e+03 pdb=" N SER Q 102 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 235 " -0.041 2.00e-02 2.50e+03 3.12e-02 1.46e+01 pdb=" CG HIS K 235 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS K 235 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS K 235 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS K 235 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS K 235 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 235 " -0.041 2.00e-02 2.50e+03 3.11e-02 1.45e+01 pdb=" CG HIS C 235 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS C 235 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 235 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS C 235 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS C 235 " -0.033 2.00e-02 2.50e+03 ... (remaining 6685 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 13727 2.89 - 3.39: 39608 3.39 - 3.90: 66114 3.90 - 4.40: 76938 4.40 - 4.90: 122795 Nonbonded interactions: 319182 Sorted by model distance: nonbonded pdb=" O ARG H 72 " pdb=" NH1 ARG H 77 " model vdw 2.388 2.520 nonbonded pdb=" O ARG P 72 " pdb=" NH1 ARG P 77 " model vdw 2.405 2.520 nonbonded pdb=" O ARG F 72 " pdb=" NH1 ARG F 77 " model vdw 2.409 2.520 nonbonded pdb=" O ARG N 72 " pdb=" NH1 ARG N 77 " model vdw 2.412 2.520 nonbonded pdb=" O ARG X 72 " pdb=" NH1 ARG X 77 " model vdw 2.427 2.520 ... (remaining 319177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'B' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'I' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'J' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'K' selection = (chain 'L' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'Q' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'S' selection = (chain 'T' and (resid 23 through 99 or resid 103 through 316)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 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: 0.030 Extract box with map and model: 13.500 Check model and map are aligned: 0.520 Set scattering table: 0.300 Process input model: 86.530 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2992 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 : 0.016 1.660 38125 Z= 0.903 Angle : 1.083 19.826 51546 Z= 0.785 Chirality : 0.066 0.335 6060 Planarity : 0.005 0.152 6688 Dihedral : 11.333 88.476 13996 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.11), residues: 4851 helix: 0.95 (0.08), residues: 3057 sheet: 2.60 (0.23), residues: 396 loop : 1.54 (0.16), residues: 1398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 895 time to evaluate : 4.073 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.5474 time to fit residues: 758.5077 Evaluate side-chains 430 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.970 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 50.0000 chunk 363 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 194 optimal weight: 6.9990 chunk 376 optimal weight: 40.0000 chunk 145 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 chunk 280 optimal weight: 10.0000 chunk 435 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN H 3 HIS ** I 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3202 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 38125 Z= 0.215 Angle : 0.558 8.243 51546 Z= 0.301 Chirality : 0.039 0.251 6060 Planarity : 0.003 0.035 6688 Dihedral : 3.780 46.119 5248 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer Outliers : 1.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.59 (0.11), residues: 4853 helix: 2.51 (0.08), residues: 3084 sheet: 3.47 (0.23), residues: 378 loop : 1.93 (0.17), residues: 1391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 437 time to evaluate : 4.142 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 outliers start: 57 outliers final: 34 residues processed: 473 average time/residue: 0.5018 time to fit residues: 388.3976 Evaluate side-chains 332 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 298 time to evaluate : 4.020 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3381 time to fit residues: 27.3646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 362 optimal weight: 0.8980 chunk 296 optimal weight: 40.0000 chunk 120 optimal weight: 30.0000 chunk 436 optimal weight: 8.9990 chunk 471 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 433 optimal weight: 50.0000 chunk 148 optimal weight: 30.0000 chunk 350 optimal weight: 3.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS C 202 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 HIS J 202 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 ASN ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 3 HIS ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS T 219 HIS U 3 HIS ** V 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 38125 Z= 0.270 Angle : 0.561 7.590 51546 Z= 0.306 Chirality : 0.038 0.157 6060 Planarity : 0.004 0.049 6688 Dihedral : 3.676 32.771 5248 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 3.29 (0.11), residues: 4853 helix: 2.36 (0.09), residues: 3069 sheet: 3.57 (0.22), residues: 378 loop : 1.52 (0.17), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 315 time to evaluate : 4.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 33 residues processed: 354 average time/residue: 0.4929 time to fit residues: 288.2061 Evaluate side-chains 307 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 274 time to evaluate : 4.021 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3488 time to fit residues: 27.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 50.0000 chunk 328 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 208 optimal weight: 40.0000 chunk 293 optimal weight: 8.9990 chunk 438 optimal weight: 4.9990 chunk 463 optimal weight: 1.9990 chunk 228 optimal weight: 6.9990 chunk 415 optimal weight: 7.9990 chunk 125 optimal weight: 0.2980 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 ASN D 202 HIS G 3 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 191 ASN T 202 HIS ** V 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3275 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 38125 Z= 0.197 Angle : 0.512 9.663 51546 Z= 0.274 Chirality : 0.037 0.155 6060 Planarity : 0.003 0.043 6688 Dihedral : 3.558 27.637 5248 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer Outliers : 1.16 % 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: 3.53 (0.11), residues: 4853 helix: 2.61 (0.09), residues: 3069 sheet: 3.62 (0.22), residues: 378 loop : 1.47 (0.17), residues: 1406 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 312 time to evaluate : 4.113 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 outliers start: 45 outliers final: 23 residues processed: 336 average time/residue: 0.4945 time to fit residues: 273.3088 Evaluate side-chains 293 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 270 time to evaluate : 4.026 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3605 time to fit residues: 20.7540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 9.9990 chunk 263 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 345 optimal weight: 50.0000 chunk 191 optimal weight: 0.6980 chunk 395 optimal weight: 50.0000 chunk 320 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 416 optimal weight: 0.9990 chunk 117 optimal weight: 30.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 ASN C 202 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 HIS D 219 HIS J 202 HIS Q 191 ASN R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3209 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 38125 Z= 0.139 Angle : 0.472 10.516 51546 Z= 0.249 Chirality : 0.037 0.175 6060 Planarity : 0.003 0.045 6688 Dihedral : 3.410 23.565 5248 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.82 % 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: 3.78 (0.12), residues: 4853 helix: 2.88 (0.09), residues: 3069 sheet: 3.34 (0.22), residues: 396 loop : 1.47 (0.17), residues: 1388 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 314 time to evaluate : 4.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 13 residues processed: 332 average time/residue: 0.4970 time to fit residues: 272.7867 Evaluate side-chains 286 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 273 time to evaluate : 4.042 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3485 time to fit residues: 14.0145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 6.9990 chunk 417 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 114 optimal weight: 50.0000 chunk 464 optimal weight: 20.0000 chunk 385 optimal weight: 0.0170 chunk 215 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 243 optimal weight: 4.9990 overall best weight: 1.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS K 191 ASN R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3201 moved from start: 0.5036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 38125 Z= 0.136 Angle : 0.486 13.167 51546 Z= 0.252 Chirality : 0.037 0.178 6060 Planarity : 0.003 0.046 6688 Dihedral : 3.325 23.390 5248 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer Outliers : 0.41 % 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: 3.81 (0.12), residues: 4853 helix: 2.90 (0.09), residues: 3075 sheet: 3.30 (0.22), residues: 396 loop : 1.49 (0.17), residues: 1382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 314 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 324 average time/residue: 0.4898 time to fit residues: 263.8301 Evaluate side-chains 289 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 282 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3572 time to fit residues: 10.3721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 9.9990 chunk 52 optimal weight: 0.0970 chunk 264 optimal weight: 50.0000 chunk 339 optimal weight: 50.0000 chunk 262 optimal weight: 30.0000 chunk 390 optimal weight: 9.9990 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 30.0000 chunk 289 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 overall best weight: 6.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS K 191 ASN M 3 HIS O 3 HIS V 3 HIS W 3 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3354 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 38125 Z= 0.280 Angle : 0.567 11.380 51546 Z= 0.308 Chirality : 0.037 0.160 6060 Planarity : 0.004 0.045 6688 Dihedral : 3.486 22.158 5248 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 1.26 % 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: 3.30 (0.11), residues: 4853 helix: 2.51 (0.09), residues: 3078 sheet: 3.07 (0.22), residues: 396 loop : 1.28 (0.17), residues: 1379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 274 time to evaluate : 4.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 30 residues processed: 296 average time/residue: 0.4877 time to fit residues: 240.3057 Evaluate side-chains 289 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3479 time to fit residues: 24.8394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 8.9990 chunk 184 optimal weight: 30.0000 chunk 276 optimal weight: 0.0070 chunk 139 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 294 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 363 optimal weight: 5.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN C 31 ASN C 219 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS L 31 ASN L 99 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3277 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 38125 Z= 0.175 Angle : 0.507 15.309 51546 Z= 0.265 Chirality : 0.037 0.156 6060 Planarity : 0.003 0.086 6688 Dihedral : 3.390 22.389 5248 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer Outliers : 0.51 % 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: 3.57 (0.12), residues: 4853 helix: 2.76 (0.09), residues: 3081 sheet: 3.02 (0.22), residues: 396 loop : 1.32 (0.17), residues: 1376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 4.095 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 outliers start: 20 outliers final: 10 residues processed: 287 average time/residue: 0.4913 time to fit residues: 233.3879 Evaluate side-chains 266 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 256 time to evaluate : 4.190 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4004 time to fit residues: 12.9484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 chunk 404 optimal weight: 30.0000 chunk 431 optimal weight: 40.0000 chunk 259 optimal weight: 2.9990 chunk 187 optimal weight: 50.0000 chunk 338 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 389 optimal weight: 5.9990 chunk 407 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 219 HIS T 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3329 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 38125 Z= 0.228 Angle : 0.538 13.661 51546 Z= 0.288 Chirality : 0.037 0.159 6060 Planarity : 0.004 0.067 6688 Dihedral : 3.449 21.171 5248 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.54 % 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: 3.38 (0.12), residues: 4853 helix: 2.63 (0.09), residues: 3078 sheet: 2.88 (0.22), residues: 396 loop : 1.22 (0.17), residues: 1379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 4.780 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 outliers start: 21 outliers final: 9 residues processed: 272 average time/residue: 0.4927 time to fit residues: 222.7459 Evaluate side-chains 264 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 4.062 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3481 time to fit residues: 11.4263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 7.9990 chunk 455 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 216 optimal weight: 50.0000 chunk 316 optimal weight: 9.9990 chunk 478 optimal weight: 0.9990 chunk 440 optimal weight: 2.9990 chunk 380 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 233 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN R 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3249 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 38125 Z= 0.145 Angle : 0.510 13.264 51546 Z= 0.265 Chirality : 0.037 0.159 6060 Planarity : 0.003 0.062 6688 Dihedral : 3.387 21.846 5248 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.12), residues: 4853 helix: 2.88 (0.09), residues: 3078 sheet: 2.91 (0.23), residues: 396 loop : 1.35 (0.17), residues: 1379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 4.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 282 average time/residue: 0.4977 time to fit residues: 233.0991 Evaluate side-chains 264 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 261 time to evaluate : 3.940 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3541 time to fit residues: 7.5091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 30.0000 chunk 405 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 56 optimal weight: 50.0000 chunk 105 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 391 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 70 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.118911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.096198 restraints weight = 144213.185| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 6.11 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 38125 Z= 0.159 Angle : 0.519 12.973 51546 Z= 0.271 Chirality : 0.037 0.160 6060 Planarity : 0.003 0.090 6688 Dihedral : 3.339 21.750 5248 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 0.18 % 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: 3.68 (0.12), residues: 4853 helix: 2.87 (0.09), residues: 3078 sheet: 2.93 (0.23), residues: 396 loop : 1.36 (0.17), residues: 1379 =============================================================================== Job complete usr+sys time: 8182.92 seconds wall clock time: 149 minutes 52.25 seconds (8992.25 seconds total)