Starting phenix.real_space_refine on Sat Mar 23 15:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/03_2024/6c9k_7437.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/03_2024/6c9k_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_7437/03_2024/6c9k_7437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/03_2024/6c9k_7437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/03_2024/6c9k_7437.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6c9k_7437/03_2024/6c9k_7437.pdb" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-dev-5265/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: 18.34, per 1000 atoms: 0.49 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: 17.75 Conformation dependent library (CDL) restraints added in 7.0 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: 3.44 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: 12.41 Time building geometry restraints manager: 18.90 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: 2.540 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: 12.570 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 94.390 Find NCS groups from input model: 2.830 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.140 ------------------------------------------------------------------------------- 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 % Allowed : 1.28 % Favored : 98.72 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 86 HIS 0.011 0.001 HIS D 268 PHE 0.003 0.000 PHE A 154 TYR 0.028 0.002 TYR A 262 ARG 0.004 0.000 ARG W 77 *********************** 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 : 4.435 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 REVERT: C 121 ILE cc_start: 0.4728 (mm) cc_final: 0.4463 (mm) REVERT: L 120 THR cc_start: 0.5082 (p) cc_final: 0.3863 (p) REVERT: Q 120 THR cc_start: 0.5185 (p) cc_final: 0.4959 (p) REVERT: T 120 THR cc_start: 0.4756 (p) cc_final: 0.4458 (p) outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.5689 time to fit residues: 788.3200 Evaluate side-chains 431 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 4.186 ------------------------------------------------------------------------------- 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** ** V 3 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: 0.3200 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38125 Z= 0.212 Angle : 0.555 8.106 51546 Z= 0.299 Chirality : 0.039 0.263 6060 Planarity : 0.003 0.035 6688 Dihedral : 3.793 45.585 5248 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.52 % Allowed : 9.71 % Favored : 88.78 % 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: 3.48 (0.23), residues: 378 loop : 1.92 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 86 HIS 0.008 0.001 HIS J 219 PHE 0.021 0.002 PHE H 35 TYR 0.017 0.002 TYR M 61 ARG 0.007 0.001 ARG N 107 *********************** 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 493 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 434 time to evaluate : 4.255 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 outliers start: 59 outliers final: 36 residues processed: 471 average time/residue: 0.4881 time to fit residues: 374.4159 Evaluate side-chains 337 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 178 ASP Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 362 optimal weight: 0.9990 chunk 296 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 chunk 436 optimal weight: 7.9990 chunk 471 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 433 optimal weight: 2.9990 chunk 148 optimal weight: 30.0000 chunk 350 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 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** ** 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** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3244 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 38125 Z= 0.197 Angle : 0.511 7.822 51546 Z= 0.276 Chirality : 0.038 0.156 6060 Planarity : 0.003 0.045 6688 Dihedral : 3.537 30.232 5248 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.21 % Allowed : 10.68 % Favored : 87.11 % 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: 3.65 (0.11), residues: 4853 helix: 2.66 (0.09), residues: 3069 sheet: 3.72 (0.22), residues: 378 loop : 1.63 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 86 HIS 0.008 0.001 HIS Q 219 PHE 0.019 0.001 PHE D 103 TYR 0.018 0.002 TYR B 64 ARG 0.006 0.001 ARG P 72 *********************** 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 433 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 347 time to evaluate : 4.248 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: I 99 ASN cc_start: 0.4391 (OUTLIER) cc_final: 0.4168 (p0) outliers start: 86 outliers final: 51 residues processed: 399 average time/residue: 0.4742 time to fit residues: 312.0656 Evaluate side-chains 346 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 294 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 75 LYS Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 178 ASP Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 120 THR Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 73 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 293 optimal weight: 30.0000 chunk 438 optimal weight: 6.9990 chunk 463 optimal weight: 0.7980 chunk 228 optimal weight: 1.9990 chunk 415 optimal weight: 0.4980 chunk 125 optimal weight: 30.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 J 202 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 191 ASN ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3202 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 38125 Z= 0.148 Angle : 0.494 10.843 51546 Z= 0.259 Chirality : 0.037 0.157 6060 Planarity : 0.003 0.043 6688 Dihedral : 3.461 27.093 5248 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.05 % Allowed : 10.89 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.80 (0.12), residues: 4853 helix: 2.83 (0.09), residues: 3072 sheet: 3.46 (0.23), residues: 396 loop : 1.59 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 86 HIS 0.007 0.001 HIS Q 219 PHE 0.025 0.001 PHE T 103 TYR 0.023 0.001 TYR T 145 ARG 0.004 0.000 ARG A 134 *********************** 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 422 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 342 time to evaluate : 4.437 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: C 121 ILE cc_start: 0.4885 (tp) cc_final: 0.4559 (tp) REVERT: S 38 THR cc_start: 0.5153 (p) cc_final: 0.4801 (p) outliers start: 80 outliers final: 48 residues processed: 386 average time/residue: 0.4837 time to fit residues: 306.7966 Evaluate side-chains 335 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 287 time to evaluate : 4.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 156 LEU Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 177 ASP Chi-restraints excluded: chain Q residue 178 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 20.0000 chunk 263 optimal weight: 30.0000 chunk 6 optimal weight: 3.9990 chunk 345 optimal weight: 50.0000 chunk 191 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 320 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 236 optimal weight: 3.9990 chunk 416 optimal weight: 9.9990 chunk 117 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 219 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 HIS J 202 HIS ** K 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 HIS P 3 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 HIS W 3 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3321 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 38125 Z= 0.247 Angle : 0.529 11.938 51546 Z= 0.291 Chirality : 0.037 0.151 6060 Planarity : 0.004 0.043 6688 Dihedral : 3.540 24.378 5248 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.41 % Allowed : 11.27 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.11), residues: 4853 helix: 2.53 (0.09), residues: 3078 sheet: 3.60 (0.21), residues: 378 loop : 1.36 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 86 HIS 0.009 0.001 HIS D 219 PHE 0.019 0.002 PHE D 103 TYR 0.016 0.002 TYR T 145 ARG 0.007 0.000 ARG I 134 *********************** 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 378 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 284 time to evaluate : 4.121 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: B 64 TYR cc_start: 0.4561 (t80) cc_final: 0.4173 (t80) outliers start: 94 outliers final: 69 residues processed: 338 average time/residue: 0.4856 time to fit residues: 269.2055 Evaluate side-chains 335 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 266 time to evaluate : 4.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 52 MET Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 93 ARG Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain O residue 79 LEU Chi-restraints excluded: chain O residue 109 MET Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 99 ASN Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 7.9990 chunk 417 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 272 optimal weight: 30.0000 chunk 114 optimal weight: 6.9990 chunk 464 optimal weight: 8.9990 chunk 385 optimal weight: 8.9990 chunk 215 optimal weight: 40.0000 chunk 38 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 243 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** T 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3325 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38125 Z= 0.228 Angle : 0.522 13.315 51546 Z= 0.282 Chirality : 0.037 0.157 6060 Planarity : 0.003 0.060 6688 Dihedral : 3.477 24.365 5248 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.36 % Allowed : 11.74 % Favored : 85.90 % 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: 3.40 (0.11), residues: 4853 helix: 2.60 (0.09), residues: 3069 sheet: 3.05 (0.22), residues: 396 loop : 1.31 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP L 86 HIS 0.007 0.001 HIS S 219 PHE 0.031 0.001 PHE L 103 TYR 0.017 0.002 TYR B 64 ARG 0.014 0.000 ARG C 134 *********************** 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 357 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 265 time to evaluate : 4.252 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: K 158 ARG cc_start: 0.5069 (mmp80) cc_final: 0.4849 (mmp80) outliers start: 92 outliers final: 69 residues processed: 323 average time/residue: 0.4965 time to fit residues: 263.2978 Evaluate side-chains 317 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 248 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 99 ASN Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 MET 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: 10.0000 chunk 264 optimal weight: 6.9990 chunk 339 optimal weight: 0.9990 chunk 262 optimal weight: 9.9990 chunk 390 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 462 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 282 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 ASN C 31 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 191 ASN L 31 ASN T 191 ASN ** T 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3325 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38125 Z= 0.218 Angle : 0.514 13.412 51546 Z= 0.277 Chirality : 0.037 0.146 6060 Planarity : 0.003 0.044 6688 Dihedral : 3.459 22.597 5248 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.26 % Allowed : 12.22 % Favored : 85.52 % 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: 2.62 (0.09), residues: 3066 sheet: 2.99 (0.22), residues: 396 loop : 1.24 (0.17), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 86 HIS 0.005 0.001 HIS R 219 PHE 0.031 0.001 PHE L 103 TYR 0.028 0.002 TYR B 64 ARG 0.011 0.000 ARG C 134 *********************** 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 344 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 256 time to evaluate : 3.938 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: K 158 ARG cc_start: 0.4925 (mmp80) cc_final: 0.4710 (mmp80) outliers start: 88 outliers final: 68 residues processed: 311 average time/residue: 0.4756 time to fit residues: 242.8681 Evaluate side-chains 318 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 250 time to evaluate : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 31 ASN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 10.0000 chunk 184 optimal weight: 50.0000 chunk 276 optimal weight: 6.9990 chunk 139 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 294 optimal weight: 6.9990 chunk 315 optimal weight: 20.0000 chunk 228 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 363 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 191 ASN L 99 ASN M 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3345 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 38125 Z= 0.236 Angle : 0.538 14.639 51546 Z= 0.287 Chirality : 0.037 0.210 6060 Planarity : 0.004 0.053 6688 Dihedral : 3.502 22.710 5248 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.18 % Allowed : 12.81 % Favored : 85.00 % 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: 3.28 (0.12), residues: 4853 helix: 2.55 (0.09), residues: 3069 sheet: 2.87 (0.22), residues: 396 loop : 1.21 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 86 HIS 0.006 0.001 HIS S 219 PHE 0.030 0.001 PHE D 103 TYR 0.027 0.002 TYR B 64 ARG 0.014 0.000 ARG C 134 *********************** 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 346 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 261 time to evaluate : 4.290 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: 85 outliers final: 66 residues processed: 312 average time/residue: 0.4939 time to fit residues: 254.4861 Evaluate side-chains 314 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 248 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 109 MET 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: 20.0000 chunk 404 optimal weight: 40.0000 chunk 431 optimal weight: 20.0000 chunk 259 optimal weight: 4.9990 chunk 187 optimal weight: 50.0000 chunk 338 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 chunk 389 optimal weight: 6.9990 chunk 407 optimal weight: 6.9990 chunk 429 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** F 3 HIS K 202 HIS L 99 ASN L 219 HIS R 191 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3355 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38125 Z= 0.243 Angle : 0.545 13.640 51546 Z= 0.293 Chirality : 0.037 0.213 6060 Planarity : 0.004 0.054 6688 Dihedral : 3.510 21.473 5248 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.13 % Allowed : 13.25 % Favored : 84.62 % 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: 3.22 (0.12), residues: 4853 helix: 2.51 (0.09), residues: 3075 sheet: 2.78 (0.23), residues: 396 loop : 1.16 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 86 HIS 0.005 0.001 HIS A 209 PHE 0.035 0.002 PHE D 103 TYR 0.029 0.002 TYR B 64 ARG 0.019 0.000 ARG C 134 *********************** 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 336 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 253 time to evaluate : 4.662 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: R 95 MET cc_start: 0.4347 (ppp) cc_final: 0.3852 (ppp) outliers start: 83 outliers final: 71 residues processed: 301 average time/residue: 0.4986 time to fit residues: 248.5002 Evaluate side-chains 314 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 243 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain W residue 109 MET Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 85 CYS Chi-restraints excluded: chain X residue 109 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 9.9990 chunk 455 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 216 optimal weight: 50.0000 chunk 316 optimal weight: 5.9990 chunk 478 optimal weight: 30.0000 chunk 440 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 294 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 O 3 HIS ** Q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 191 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3387 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38125 Z= 0.277 Angle : 0.584 12.850 51546 Z= 0.314 Chirality : 0.037 0.165 6060 Planarity : 0.004 0.072 6688 Dihedral : 3.628 24.980 5248 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.03 % Allowed : 13.56 % Favored : 84.41 % 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: 2.99 (0.12), residues: 4853 helix: 2.32 (0.09), residues: 3075 sheet: 2.68 (0.23), residues: 396 loop : 1.11 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 86 HIS 0.006 0.001 HIS T 46 PHE 0.018 0.002 PHE D 136 TYR 0.025 0.002 TYR B 64 ARG 0.017 0.001 ARG C 134 ********************** 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 330 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 251 time to evaluate : 4.599 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: R 95 MET cc_start: 0.4438 (ppp) cc_final: 0.3955 (ppp) outliers start: 79 outliers final: 70 residues processed: 297 average time/residue: 0.4902 time to fit residues: 240.6136 Evaluate side-chains 309 residues out of total 3894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 239 time to evaluate : 4.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 178 ASP Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 52 MET Chi-restraints excluded: chain L residue 86 TRP Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain N residue 5 VAL Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 109 MET Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 67 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 101 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain W residue 109 MET Chi-restraints excluded: chain X residue 73 ASP Chi-restraints excluded: chain X residue 85 CYS Chi-restraints excluded: chain X residue 109 MET 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: 50.0000 chunk 116 optimal weight: 10.0000 chunk 351 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 105 optimal weight: 20.0000 chunk 381 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 391 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 overall best weight: 2.0784 ------------------------------------------------------------------------------- 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** D 202 HIS E 24 GLN K 202 HIS L 31 ASN ** Q 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.115885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.092509 restraints weight = 149641.710| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 6.36 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.6091 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= 0.152 Angle : 0.508 12.586 51546 Z= 0.267 Chirality : 0.038 0.164 6060 Planarity : 0.003 0.071 6688 Dihedral : 3.446 23.381 5248 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.67 % Allowed : 14.25 % Favored : 84.08 % 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: 3.59 (0.12), residues: 4853 helix: 2.81 (0.09), residues: 3078 sheet: 2.84 (0.23), residues: 396 loop : 1.31 (0.18), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 86 HIS 0.004 0.001 HIS A 209 PHE 0.022 0.001 PHE J 136 TYR 0.027 0.001 TYR B 64 ARG 0.017 0.000 ARG J 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8961.24 seconds wall clock time: 163 minutes 46.15 seconds (9826.15 seconds total)