Starting phenix.real_space_refine on Wed Feb 14 19:20:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpk_0749/02_2024/6kpk_0749.pdb" } resolution = 2.3 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= -0.004 sd= 0.394 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: 6 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 20004 2.51 5 N 5076 2.21 5 O 5760 1.98 5 H 31225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 62209 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 20.50, per 1000 atoms: 0.33 Number of scatterers: 62209 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5760 8.00 N 5076 7.00 C 20004 6.00 H 31225 1.00 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: 40.37 Conformation dependent library (CDL) restraints added in 5.0 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 12 sheets defined 66.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 48 through 57 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.572A pdb=" N VAL A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET A 137 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU A 226 " --> pdb=" O GLU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS A 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'A' and resid 313 through 326 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 48 through 57 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL B 86 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET B 137 " --> pdb=" O GLY B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.946A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.948A pdb=" N LEU B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS B 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.613A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'C' and resid 24 through 37 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.572A pdb=" N VAL C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET C 137 " --> pdb=" O GLY C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 171 Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 229 removed outlier: 3.948A pdb=" N LEU C 226 " --> pdb=" O GLU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS C 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.615A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 313 through 326 Processing helix chain 'D' and resid 24 through 37 Processing helix chain 'D' and resid 48 through 57 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL D 86 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 133 through 141 removed outlier: 3.689A pdb=" N MET D 137 " --> pdb=" O GLY D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.946A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU D 226 " --> pdb=" O GLU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS D 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 Processing helix chain 'D' and resid 313 through 326 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL E 86 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 Processing helix chain 'E' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU E 226 " --> pdb=" O GLU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS E 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.613A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 Processing helix chain 'E' and resid 313 through 326 Processing helix chain 'F' and resid 24 through 37 Processing helix chain 'F' and resid 48 through 57 Processing helix chain 'F' and resid 63 through 71 Processing helix chain 'F' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL F 86 " --> pdb=" O VAL F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 Processing helix chain 'F' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET F 137 " --> pdb=" O GLY F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.946A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU F 226 " --> pdb=" O GLU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS F 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 Processing helix chain 'F' and resid 313 through 326 Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 63 through 71 Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.572A pdb=" N VAL G 86 " --> pdb=" O VAL G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL G 94 " --> pdb=" O LYS G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 Processing helix chain 'G' and resid 133 through 141 removed outlier: 3.689A pdb=" N MET G 137 " --> pdb=" O GLY G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 171 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU G 226 " --> pdb=" O GLU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS G 252 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 268 Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 Processing helix chain 'G' and resid 313 through 326 Processing helix chain 'H' and resid 24 through 37 Processing helix chain 'H' and resid 48 through 57 Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL H 86 " --> pdb=" O VAL H 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL H 94 " --> pdb=" O LYS H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 Processing helix chain 'H' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET H 137 " --> pdb=" O GLY H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 171 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.946A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 217 removed outlier: 3.595A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU H 226 " --> pdb=" O GLU H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU H 236 " --> pdb=" O GLY H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS H 252 " --> pdb=" O GLN H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 268 Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 Processing helix chain 'H' and resid 313 through 326 Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 48 through 57 Processing helix chain 'I' and resid 63 through 71 Processing helix chain 'I' and resid 82 through 90 removed outlier: 3.572A pdb=" N VAL I 86 " --> pdb=" O VAL I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL I 94 " --> pdb=" O LYS I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET I 137 " --> pdb=" O GLY I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.944A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.595A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU I 226 " --> pdb=" O GLU I 222 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU I 236 " --> pdb=" O GLY I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS I 252 " --> pdb=" O GLN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 268 Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 Processing helix chain 'I' and resid 313 through 326 Processing helix chain 'J' and resid 24 through 37 Processing helix chain 'J' and resid 48 through 57 Processing helix chain 'J' and resid 63 through 71 Processing helix chain 'J' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL J 86 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL J 94 " --> pdb=" O LYS J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 Processing helix chain 'J' and resid 133 through 141 removed outlier: 3.689A pdb=" N MET J 137 " --> pdb=" O GLY J 133 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 171 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.595A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU J 226 " --> pdb=" O GLU J 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU J 236 " --> pdb=" O GLY J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS J 252 " --> pdb=" O GLN J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 268 Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.768A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 Processing helix chain 'J' and resid 313 through 326 Processing helix chain 'K' and resid 24 through 37 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 63 through 71 Processing helix chain 'K' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL K 86 " --> pdb=" O VAL K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 4.396A pdb=" N VAL K 94 " --> pdb=" O LYS K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 Processing helix chain 'K' and resid 133 through 141 removed outlier: 3.690A pdb=" N MET K 137 " --> pdb=" O GLY K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 171 Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.946A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 217 removed outlier: 3.595A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU K 226 " --> pdb=" O GLU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 232 through 245 removed outlier: 3.577A pdb=" N GLU K 236 " --> pdb=" O GLY K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 253 removed outlier: 3.548A pdb=" N HIS K 252 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 268 Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 Processing helix chain 'K' and resid 313 through 326 Processing helix chain 'L' and resid 24 through 37 Processing helix chain 'L' and resid 48 through 57 Processing helix chain 'L' and resid 63 through 71 Processing helix chain 'L' and resid 82 through 90 removed outlier: 3.573A pdb=" N VAL L 86 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 97 removed outlier: 4.397A pdb=" N VAL L 94 " --> pdb=" O LYS L 90 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 Processing helix chain 'L' and resid 133 through 141 removed outlier: 3.689A pdb=" N MET L 137 " --> pdb=" O GLY L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 171 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.945A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 217 removed outlier: 3.594A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 229 removed outlier: 3.947A pdb=" N LEU L 226 " --> pdb=" O GLU L 222 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 245 removed outlier: 3.576A pdb=" N GLU L 236 " --> pdb=" O GLY L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 253 removed outlier: 3.549A pdb=" N HIS L 252 " --> pdb=" O GLN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 268 Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.769A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.614A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 Processing helix chain 'L' and resid 313 through 326 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.492A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE A 101 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE A 125 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 103 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL A 127 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE A 105 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE B 101 " --> pdb=" O ASP B 123 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE B 125 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU B 103 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL B 127 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE B 105 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE C 101 " --> pdb=" O ASP C 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE C 125 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 103 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL C 127 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE C 105 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE D 101 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE D 125 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 103 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL D 127 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE D 105 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE E 101 " --> pdb=" O ASP E 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE E 125 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 103 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 127 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE E 105 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE F 101 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE F 125 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU F 103 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 127 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE F 105 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE G 101 " --> pdb=" O ASP G 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE G 125 " --> pdb=" O PHE G 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU G 103 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL G 127 " --> pdb=" O LEU G 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE G 105 " --> pdb=" O VAL G 127 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE H 101 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE H 125 " --> pdb=" O PHE H 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU H 103 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL H 127 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE H 105 " --> pdb=" O VAL H 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 4 through 5 removed outlier: 6.492A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE I 101 " --> pdb=" O ASP I 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE I 125 " --> pdb=" O PHE I 101 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU I 103 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL I 127 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE I 105 " --> pdb=" O VAL I 127 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE J 101 " --> pdb=" O ASP J 123 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE J 125 " --> pdb=" O PHE J 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU J 103 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL J 127 " --> pdb=" O LEU J 103 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE J 105 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 4 through 5 removed outlier: 6.493A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE K 101 " --> pdb=" O ASP K 123 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE K 125 " --> pdb=" O PHE K 101 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU K 103 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL K 127 " --> pdb=" O LEU K 103 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE K 105 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 5 removed outlier: 6.494A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N PHE L 101 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ILE L 125 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU L 103 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL L 127 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE L 105 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) 1824 hydrogen bonds defined for protein. 5328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.58 Time building geometry restraints manager: 42.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 31209 1.02 - 1.22: 16 1.22 - 1.41: 12933 1.41 - 1.61: 18435 1.61 - 1.80: 228 Bond restraints: 62821 Sorted by residual: bond pdb=" CG MET L 34 " pdb=" HG3 MET L 34 " ideal model delta sigma weight residual 0.970 1.063 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CG GLU J 233 " pdb=" HG2 GLU J 233 " ideal model delta sigma weight residual 0.970 1.057 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" CG MET L 34 " pdb=" HG2 MET L 34 " ideal model delta sigma weight residual 0.970 1.046 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" CG GLU C 233 " pdb=" HG2 GLU C 233 " ideal model delta sigma weight residual 0.970 1.026 -0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" CG GLU L 233 " pdb=" HG3 GLU L 233 " ideal model delta sigma weight residual 0.970 0.922 0.048 2.00e-02 2.50e+03 5.87e+00 ... (remaining 62816 not shown) Histogram of bond angle deviations from ideal: 53.24 - 69.46: 21 69.46 - 85.69: 244 85.69 - 101.91: 152 101.91 - 118.13: 85180 118.13 - 134.36: 28389 Bond angle restraints: 113986 Sorted by residual: angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 65.86 59.07 3.00e+00 1.11e-01 3.88e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 55.76 58.87 3.00e+00 1.11e-01 3.85e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.53 55.95 58.58 3.00e+00 1.11e-01 3.81e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.53 55.98 58.54 3.00e+00 1.11e-01 3.81e+02 angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.83 66.53 58.30 3.00e+00 1.11e-01 3.78e+02 ... (remaining 113981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 25331 14.76 - 29.52: 2819 29.52 - 44.29: 748 44.29 - 59.05: 295 59.05 - 73.81: 28 Dihedral angle restraints: 29221 sinusoidal: 15868 harmonic: 13353 Sorted by residual: dihedral pdb=" CA LYS L 3 " pdb=" C LYS L 3 " pdb=" N THR L 4 " pdb=" CA THR L 4 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS K 3 " pdb=" C LYS K 3 " pdb=" N THR K 4 " pdb=" CA THR K 4 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS G 3 " pdb=" C LYS G 3 " pdb=" N THR G 4 " pdb=" CA THR G 4 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 29218 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3797 0.065 - 0.131: 751 0.131 - 0.196: 48 0.196 - 0.262: 36 0.262 - 0.327: 36 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CB VAL C 127 " pdb=" CA VAL C 127 " pdb=" CG1 VAL C 127 " pdb=" CG2 VAL C 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB VAL D 127 " pdb=" CA VAL D 127 " pdb=" CG1 VAL D 127 " pdb=" CG2 VAL D 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CB VAL B 127 " pdb=" CA VAL B 127 " pdb=" CG1 VAL B 127 " pdb=" CG2 VAL B 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 4665 not shown) Planarity restraints: 9208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 146 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO B 147 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR L 146 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.97e+00 pdb=" N PRO L 147 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 147 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 147 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 146 " 0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO A 147 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " 0.031 5.00e-02 4.00e+02 ... (remaining 9205 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.02: 806 2.02 - 2.66: 90536 2.66 - 3.31: 176068 3.31 - 3.95: 228467 3.95 - 4.60: 375064 Nonbonded interactions: 870941 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.371 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.426 1.816 nonbonded pdb=" H LYS J 159 " pdb=" HA LYS J 159 " model vdw 1.517 1.816 nonbonded pdb=" H LYS K 56 " pdb=" HA LYS K 56 " model vdw 1.518 1.816 nonbonded pdb=" H LYS E 159 " pdb=" HA LYS E 159 " model vdw 1.519 1.816 ... (remaining 870936 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 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'C' and (resid 2 through 329 or resid 401)) selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401)) selection = (chain 'L' and (resid 2 through 329 or resid 401)) } 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.680 Extract box with map and model: 10.990 Check model and map are aligned: 0.700 Set scattering table: 0.430 Process input model: 155.330 Find NCS groups from input model: 2.750 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.006 0.056 31596 Z= 0.393 Angle : 0.709 13.124 42660 Z= 0.395 Chirality : 0.057 0.327 4668 Planarity : 0.004 0.056 5424 Dihedral : 12.552 73.810 11736 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.37 % Allowed : 2.65 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -3.66 (0.11), residues: 3912 helix: -2.04 (0.09), residues: 2364 sheet: -2.09 (0.19), residues: 504 loop : -2.96 (0.14), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 198 HIS 0.004 0.001 HIS B 196 PHE 0.011 0.002 PHE J 303 TYR 0.009 0.001 TYR E 217 ARG 0.001 0.000 ARG E 305 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 471 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8860 (mttt) cc_final: 0.8549 (mttm) REVERT: C 215 LYS cc_start: 0.8765 (mttt) cc_final: 0.8553 (mttm) REVERT: C 274 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7529 (mtm-85) REVERT: D 215 LYS cc_start: 0.8864 (mttt) cc_final: 0.8528 (mttm) REVERT: F 215 LYS cc_start: 0.8791 (mttt) cc_final: 0.8482 (mttm) REVERT: G 215 LYS cc_start: 0.8874 (mttt) cc_final: 0.8545 (mttm) REVERT: H 215 LYS cc_start: 0.8890 (mttt) cc_final: 0.8588 (mttm) REVERT: I 215 LYS cc_start: 0.8879 (mttt) cc_final: 0.8540 (mttm) REVERT: J 215 LYS cc_start: 0.8834 (mttt) cc_final: 0.8533 (mttm) REVERT: L 215 LYS cc_start: 0.8773 (mttt) cc_final: 0.8540 (mttm) outliers start: 12 outliers final: 0 residues processed: 483 average time/residue: 3.5034 time to fit residues: 1917.6224 Evaluate side-chains 290 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 290 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 1.9990 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 196 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 7.9990 chunk 348 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 30 GLN A 140 HIS A 278 ASN B 26 GLN B 30 GLN B 140 HIS B 278 ASN C 30 GLN C 278 ASN D 26 GLN D 30 GLN D 96 GLN D 140 HIS D 278 ASN E 26 GLN E 30 GLN E 140 HIS E 278 ASN F 26 GLN F 30 GLN F 140 HIS F 278 ASN G 30 GLN G 278 ASN H 26 GLN H 30 GLN H 140 HIS H 278 ASN I 26 GLN I 30 GLN I 96 GLN I 140 HIS I 278 ASN J 26 GLN J 30 GLN J 278 ASN K 26 GLN K 30 GLN K 140 HIS K 278 ASN L 30 GLN L 278 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31596 Z= 0.248 Angle : 0.723 20.759 42660 Z= 0.377 Chirality : 0.127 1.719 4668 Planarity : 0.004 0.046 5424 Dihedral : 4.221 14.999 4284 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.97 % Allowed : 8.86 % Favored : 90.17 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -1.32 (0.12), residues: 3912 helix: -0.09 (0.10), residues: 2484 sheet: -1.57 (0.19), residues: 504 loop : -2.31 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 198 HIS 0.004 0.001 HIS B 196 PHE 0.013 0.002 PHE J 184 TYR 0.008 0.001 TYR C 217 ARG 0.005 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 295 time to evaluate : 3.737 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 outliers start: 31 outliers final: 8 residues processed: 326 average time/residue: 2.9452 time to fit residues: 1117.7968 Evaluate side-chains 264 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 256 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 320 LYS Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain K residue 320 LYS Chi-restraints excluded: chain L residue 17 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 0.7980 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 26 GLN D 26 GLN E 26 GLN F 26 GLN G 26 GLN H 26 GLN I 26 GLN J 26 GLN K 26 GLN L 26 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 31596 Z= 0.227 Angle : 0.665 19.470 42660 Z= 0.346 Chirality : 0.125 1.664 4668 Planarity : 0.004 0.035 5424 Dihedral : 3.923 15.420 4284 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.25 % Allowed : 9.43 % Favored : 89.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3912 helix: 0.88 (0.10), residues: 2484 sheet: -1.19 (0.21), residues: 504 loop : -1.92 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.008 0.002 HIS K 196 PHE 0.009 0.001 PHE G 288 TYR 0.009 0.001 TYR K 217 ARG 0.004 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 290 time to evaluate : 3.756 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 outliers start: 40 outliers final: 13 residues processed: 326 average time/residue: 2.6569 time to fit residues: 1020.3347 Evaluate side-chains 262 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain K residue 320 LYS Chi-restraints excluded: chain L residue 17 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 4.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN E 26 GLN F 26 GLN G 26 GLN G 140 HIS H 26 GLN I 26 GLN J 26 GLN J 140 HIS L 26 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31596 Z= 0.304 Angle : 0.686 20.096 42660 Z= 0.359 Chirality : 0.129 1.733 4668 Planarity : 0.004 0.036 5424 Dihedral : 3.959 15.889 4284 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.91 % Allowed : 10.89 % Favored : 88.20 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.13), residues: 3912 helix: 1.05 (0.10), residues: 2472 sheet: -1.13 (0.21), residues: 516 loop : -1.58 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 198 HIS 0.009 0.002 HIS F 196 PHE 0.012 0.002 PHE J 288 TYR 0.009 0.001 TYR D 217 ARG 0.003 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 283 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 310 average time/residue: 2.8579 time to fit residues: 1037.3510 Evaluate side-chains 281 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 3.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 GLN J 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.242 Angle : 0.662 20.123 42660 Z= 0.344 Chirality : 0.129 1.751 4668 Planarity : 0.003 0.036 5424 Dihedral : 3.899 15.698 4284 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.75 % Allowed : 11.86 % Favored : 87.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.13), residues: 3912 helix: 1.20 (0.10), residues: 2472 sheet: -0.98 (0.22), residues: 516 loop : -1.36 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 198 HIS 0.005 0.001 HIS H 196 PHE 0.011 0.002 PHE G 288 TYR 0.008 0.001 TYR E 217 ARG 0.001 0.000 ARG G 274 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 20 residues processed: 292 average time/residue: 2.9633 time to fit residues: 1009.5218 Evaluate side-chains 277 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 257 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31596 Z= 0.228 Angle : 0.662 20.255 42660 Z= 0.342 Chirality : 0.129 1.744 4668 Planarity : 0.003 0.038 5424 Dihedral : 3.826 15.687 4284 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.91 % Allowed : 12.02 % Favored : 87.08 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3912 helix: 1.35 (0.10), residues: 2484 sheet: -0.83 (0.22), residues: 516 loop : -1.14 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.006 0.001 HIS B 196 PHE 0.010 0.002 PHE K 288 TYR 0.007 0.001 TYR G 217 ARG 0.002 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 274 time to evaluate : 4.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 298 average time/residue: 2.9546 time to fit residues: 1022.8193 Evaluate side-chains 278 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 370 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 31596 Z= 0.259 Angle : 0.678 20.173 42660 Z= 0.349 Chirality : 0.129 1.752 4668 Planarity : 0.003 0.038 5424 Dihedral : 3.849 15.724 4284 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.19 % Allowed : 12.20 % Favored : 86.61 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.14), residues: 3912 helix: 1.34 (0.10), residues: 2496 sheet: -0.71 (0.22), residues: 516 loop : -1.05 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 198 HIS 0.006 0.001 HIS J 196 PHE 0.011 0.002 PHE K 288 TYR 0.008 0.001 TYR I 217 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 275 time to evaluate : 4.019 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: F 154 GLN cc_start: 0.8651 (tt0) cc_final: 0.8302 (tt0) outliers start: 38 outliers final: 19 residues processed: 311 average time/residue: 2.9912 time to fit residues: 1083.0857 Evaluate side-chains 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 264 time to evaluate : 3.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31596 Z= 0.202 Angle : 0.665 20.383 42660 Z= 0.339 Chirality : 0.129 1.749 4668 Planarity : 0.003 0.035 5424 Dihedral : 3.769 15.579 4284 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.69 % Allowed : 12.89 % Favored : 86.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3912 helix: 1.48 (0.10), residues: 2508 sheet: -0.65 (0.23), residues: 516 loop : -0.94 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.004 0.001 HIS C 196 PHE 0.009 0.001 PHE K 288 TYR 0.006 0.001 TYR H 229 ARG 0.001 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 282 time to evaluate : 3.742 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: E 249 GLN cc_start: 0.9381 (OUTLIER) cc_final: 0.9170 (pp30) outliers start: 22 outliers final: 16 residues processed: 298 average time/residue: 3.1136 time to fit residues: 1080.6446 Evaluate side-chains 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 95 LEU Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 323 optimal weight: 1.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 326 optimal weight: 0.2980 chunk 343 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31596 Z= 0.245 Angle : 0.675 20.241 42660 Z= 0.346 Chirality : 0.129 1.752 4668 Planarity : 0.003 0.034 5424 Dihedral : 3.797 15.741 4284 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.66 % Allowed : 13.08 % Favored : 86.27 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.14), residues: 3912 helix: 1.48 (0.10), residues: 2496 sheet: -0.59 (0.23), residues: 516 loop : -0.91 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.005 0.001 HIS J 196 PHE 0.011 0.002 PHE F 288 TYR 0.008 0.001 TYR G 217 ARG 0.001 0.000 ARG L 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 274 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLN cc_start: 0.8693 (tt0) cc_final: 0.8359 (tt0) REVERT: C 154 GLN cc_start: 0.8688 (tt0) cc_final: 0.8342 (tt0) REVERT: D 154 GLN cc_start: 0.8685 (tt0) cc_final: 0.8365 (tt0) REVERT: H 154 GLN cc_start: 0.8681 (tt0) cc_final: 0.8346 (tt0) REVERT: H 249 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.9161 (pp30) REVERT: J 154 GLN cc_start: 0.8685 (tt0) cc_final: 0.8353 (tt0) REVERT: K 154 GLN cc_start: 0.8690 (tt0) cc_final: 0.8358 (tt0) REVERT: L 154 GLN cc_start: 0.8678 (tt0) cc_final: 0.8334 (tt0) REVERT: L 249 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.9201 (pp30) outliers start: 21 outliers final: 16 residues processed: 293 average time/residue: 3.0865 time to fit residues: 1044.5729 Evaluate side-chains 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 265 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 249 GLN Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 249 GLN Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 31596 Z= 0.314 Angle : 0.699 20.070 42660 Z= 0.362 Chirality : 0.130 1.761 4668 Planarity : 0.003 0.036 5424 Dihedral : 3.925 16.330 4284 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.59 % Allowed : 13.08 % Favored : 86.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3912 helix: 1.35 (0.10), residues: 2496 sheet: -0.56 (0.23), residues: 516 loop : -0.91 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 198 HIS 0.007 0.002 HIS L 196 PHE 0.013 0.002 PHE E 288 TYR 0.009 0.001 TYR G 217 ARG 0.002 0.000 ARG G 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 3.799 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: I 154 GLN cc_start: 0.8729 (tt0) cc_final: 0.8151 (tt0) REVERT: L 154 GLN cc_start: 0.8663 (tt0) cc_final: 0.8079 (tt0) REVERT: L 249 GLN cc_start: 0.9420 (OUTLIER) cc_final: 0.9190 (pp30) outliers start: 19 outliers final: 16 residues processed: 285 average time/residue: 3.1458 time to fit residues: 1041.0068 Evaluate side-chains 283 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 266 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain E residue 308 GLU Chi-restraints excluded: chain F residue 308 GLU Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 308 GLU Chi-restraints excluded: chain I residue 308 GLU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 308 GLU Chi-restraints excluded: chain L residue 249 GLN Chi-restraints excluded: chain L residue 308 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 1.9990 chunk 324 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.0050 chunk 127 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.085320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.055696 restraints weight = 186602.947| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.87 r_work: 0.2497 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31596 Z= 0.227 Angle : 0.674 20.289 42660 Z= 0.345 Chirality : 0.129 1.746 4668 Planarity : 0.003 0.034 5424 Dihedral : 3.837 16.285 4284 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.56 % Allowed : 13.11 % Favored : 86.33 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.14), residues: 3912 helix: 1.48 (0.10), residues: 2496 sheet: -0.55 (0.23), residues: 516 loop : -0.80 (0.23), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 198 HIS 0.004 0.001 HIS C 196 PHE 0.010 0.002 PHE L 288 TYR 0.007 0.001 TYR H 229 ARG 0.002 0.000 ARG J 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18092.80 seconds wall clock time: 310 minutes 58.71 seconds (18658.71 seconds total)