Starting phenix.real_space_refine on Mon Jul 6 02:29:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihp_35451/07_2026/8ihp_35451.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 254 5.16 5 C 20354 2.51 5 N 5604 2.21 5 O 6122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 266 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32337 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "B" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "C" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "D" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "E" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "F" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "G" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "H" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "I" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "J" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3250 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "K" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "L" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "M" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "N" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "O" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 298 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.13, per 1000 atoms: 0.22 Number of scatterers: 32337 At special positions: 0 Unit cell: (201.4, 204.58, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 254 16.00 O 6122 8.00 N 5604 7.00 C 20354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=61, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 28 " distance=2.03 Simple disulfide: pdb=" SG CYS A 91 " - pdb=" SG CYS A 105 " distance=2.02 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 265 " distance=1.79 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 376 " distance=2.03 Simple disulfide: pdb=" SG CYS B 306 " - pdb=" SG CYS B 380 " distance=2.03 Simple disulfide: pdb=" SG CYS B 328 " - pdb=" SG CYS B 370 " distance=2.93 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 125 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 28 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.02 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 265 " distance=2.10 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 225 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.02 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 19 " - pdb=" SG CYS G 125 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 28 " distance=2.03 Simple disulfide: pdb=" SG CYS G 91 " - pdb=" SG CYS G 105 " distance=2.02 Simple disulfide: pdb=" SG CYS G 153 " - pdb=" SG CYS G 265 " distance=2.04 Simple disulfide: pdb=" SG CYS G 201 " - pdb=" SG CYS G 225 " distance=2.03 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.04 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.02 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 28 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 265 " distance=1.58 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.02 Simple disulfide: pdb=" SG CYS K 49 " - pdb=" SG CYS K 114 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 94 " distance=2.03 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 259 " - pdb=" SG CYS K 271 " distance=2.03 Simple disulfide: pdb=" SG CYS K 301 " - pdb=" SG CYS K 376 " distance=2.03 Simple disulfide: pdb=" SG CYS K 306 " - pdb=" SG CYS K 380 " distance=2.02 Simple disulfide: pdb=" SG CYS K 328 " - pdb=" SG CYS K 370 " distance=2.03 Simple disulfide: pdb=" SG CYS M 113 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 120 " - pdb=" SG CYS M 140 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 149 " distance=2.03 Simple disulfide: pdb=" SG CYS N 113 " - pdb=" SG CYS N 127 " distance=2.04 Simple disulfide: pdb=" SG CYS N 120 " - pdb=" SG CYS N 140 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 149 " distance=2.03 Simple disulfide: pdb=" SG CYS O 113 " - pdb=" SG CYS O 127 " distance=2.03 Simple disulfide: pdb=" SG CYS O 120 " - pdb=" SG CYS O 140 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied NAG-ASN " NAG A 500 " - " ASN A 200 " " NAG A 501 " - " ASN A 262 " " NAG B 500 " - " ASN B 141 " " NAG D 500 " - " ASN D 200 " " NAG D 501 " - " ASN D 262 " " NAG E 500 " - " ASN E 141 " " NAG G 500 " - " ASN G 200 " " NAG G 501 " - " ASN G 262 " " NAG H 500 " - " ASN H 141 " " NAG J 500 " - " ASN J 200 " " NAG J 501 " - " ASN J 262 " " NAG K 500 " - " ASN K 141 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7736 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 86 sheets defined 14.3% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.142A pdb=" N PHE A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 362 through 402 Proline residue: A 398 - end of helix removed outlier: 3.518A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.883A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.615A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.630A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 287' Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 404 through 437 removed outlier: 3.661A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 9 through 12 removed outlier: 3.531A pdb=" N THR D 12 " --> pdb=" O TYR D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.856A pdb=" N LEU D 180 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 181 " --> pdb=" O ARG D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 350 through 360 removed outlier: 3.595A pdb=" N VAL D 355 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 397 Processing helix chain 'D' and resid 398 through 401 Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.780A pdb=" N LEU D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.562A pdb=" N LYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.688A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 404 through 436 Processing helix chain 'F' and resid 107 through 119 removed outlier: 3.767A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.643A pdb=" N MET F 177 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER F 179 " --> pdb=" O HIS F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.522A pdb=" N GLN G 356 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 401 Proline residue: G 398 - end of helix Processing helix chain 'G' and resid 411 through 416 removed outlier: 3.993A pdb=" N CYS G 415 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 411 through 416' Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.568A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.778A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 removed outlier: 3.525A pdb=" N ALA H 286 " --> pdb=" O PRO H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 435 removed outlier: 3.819A pdb=" N TRP H 409 " --> pdb=" O THR H 405 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.794A pdb=" N MET I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE I 115 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 Processing helix chain 'I' and resid 174 through 179 removed outlier: 4.112A pdb=" N SER I 179 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 removed outlier: 3.868A pdb=" N ALA J 11 " --> pdb=" O ASN J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 350 through 360 removed outlier: 3.581A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 397 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'K' and resid 238 through 247 removed outlier: 3.641A pdb=" N LYS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.618A pdb=" N GLY K 258 " --> pdb=" O ALA K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 287 Processing helix chain 'K' and resid 289 through 293 Processing helix chain 'K' and resid 404 through 436 removed outlier: 3.573A pdb=" N TRP K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 410 " --> pdb=" O ALA K 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.312A pdb=" N GLU L 116 " --> pdb=" O CYS L 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN L 117 " --> pdb=" O MET L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.873A pdb=" N LYS L 157 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 133 No H-bonds generated for 'chain 'M' and resid 131 through 133' Processing helix chain 'M' and resid 143 through 147 removed outlier: 3.753A pdb=" N GLU M 146 " --> pdb=" O GLY M 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU M 147 " --> pdb=" O GLU M 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 143 through 147' Processing helix chain 'N' and resid 131 through 133 No H-bonds generated for 'chain 'N' and resid 131 through 133' Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.234A pdb=" N LYS A 66 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 156 Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.600A pdb=" N VAL A 208 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N CYS A 201 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY A 206 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'A' and resid 274 through 277 Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.657A pdb=" N GLN B 160 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.950A pdb=" N LYS B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 36 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 130 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.630A pdb=" N THR B 288 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.013A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 100 through 110 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AB7, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 306 removed outlier: 5.476A pdb=" N ASP B 298 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 315 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AC3, first strand: chain 'C' and resid 149 through 150 removed outlier: 6.380A pdb=" N PHE C 121 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR C 132 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 123 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 130 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR C 132 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 194 removed outlier: 4.067A pdb=" N GLY C 191 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 202 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 199 " --> pdb=" O PRO C 210 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 210 current: chain 'C' and resid 232 through 238 removed outlier: 7.153A pdb=" N ALA C 232 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TRP C 251 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL C 234 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 249 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 38 removed outlier: 8.328A pdb=" N ILE D 34 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 51 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 156 Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.790A pdb=" N MET D 215 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AD3, first strand: chain 'D' and resid 274 through 277 Processing sheet with id=AD4, first strand: chain 'D' and resid 306 through 310 removed outlier: 3.504A pdb=" N TYR D 296 " --> pdb=" O HIS D 306 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.668A pdb=" N GLN E 160 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.582A pdb=" N TYR E 15 " --> pdb=" O MET E 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 27 through 33 current: chain 'E' and resid 119 through 137 removed outlier: 3.767A pdb=" N TYR E 137 " --> pdb=" O VAL E 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 147 current: chain 'E' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 185 current: chain 'E' and resid 268 through 269 Processing sheet with id=AD7, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 100 through 110 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AD9, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'E' and resid 296 through 306 removed outlier: 5.980A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 326 through 329 Processing sheet with id=AE3, first strand: chain 'E' and resid 364 through 367 Processing sheet with id=AE4, first strand: chain 'F' and resid 149 through 150 removed outlier: 6.352A pdb=" N PHE F 121 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR F 132 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 123 " --> pdb=" O THR F 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR F 132 " --> pdb=" O PRO F 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 183 through 184 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 184 current: chain 'F' and resid 198 through 203 removed outlier: 9.162A pdb=" N ALA F 199 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 201 " --> pdb=" O THR F 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 206 through 210 current: chain 'F' and resid 229 through 240 removed outlier: 7.901A pdb=" N ALA F 232 " --> pdb=" O TRP F 251 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP F 251 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL F 234 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL F 249 " --> pdb=" O VAL F 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AE7, first strand: chain 'G' and resid 36 through 38 removed outlier: 9.619A pdb=" N SER G 51 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA G 70 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS G 66 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 69 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=AE9, first strand: chain 'G' and resid 149 through 156 Processing sheet with id=AF1, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AF2, first strand: chain 'G' and resid 175 through 177 removed outlier: 4.612A pdb=" N VAL G 227 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AF4, first strand: chain 'G' and resid 274 through 277 Processing sheet with id=AF5, first strand: chain 'G' and resid 306 through 310 Processing sheet with id=AF6, first strand: chain 'H' and resid 2 through 8 removed outlier: 3.536A pdb=" N GLN H 160 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 159 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 15 through 19 removed outlier: 3.716A pdb=" N TYR H 15 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR H 41 " --> pdb=" O HIS H 125 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 137 " --> pdb=" O VAL H 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 184 through 185 Processing sheet with id=AF8, first strand: chain 'H' and resid 24 through 25 removed outlier: 4.678A pdb=" N THR H 288 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 100 through 110 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AG2, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AG3, first strand: chain 'H' and resid 260 through 262 removed outlier: 4.142A pdb=" N ARG H 267 " --> pdb=" O LYS H 262 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 297 through 306 removed outlier: 4.175A pdb=" N LEU H 299 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR H 319 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS H 301 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR H 317 " --> pdb=" O CYS H 301 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL H 303 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL H 315 " --> pdb=" O VAL H 303 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AG6, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.559A pdb=" N LYS I 124 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 149 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 134 through 135 Processing sheet with id=AG8, first strand: chain 'I' and resid 239 through 240 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 239 through 240 current: chain 'I' and resid 199 through 203 removed outlier: 4.144A pdb=" N GLY I 191 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ALA I 232 " --> pdb=" O TRP I 251 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N TRP I 251 " --> pdb=" O ALA I 232 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'J' and resid 37 through 38 removed outlier: 7.167A pdb=" N PHE J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR J 96 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU J 102 " --> pdb=" O HIS J 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 53 through 56 removed outlier: 6.346A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH4, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AH6, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH7, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AH8, first strand: chain 'J' and resid 274 through 278 removed outlier: 4.085A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 306 through 310 Processing sheet with id=AI1, first strand: chain 'K' and resid 2 through 8 Processing sheet with id=AI2, first strand: chain 'K' and resid 15 through 19 removed outlier: 3.509A pdb=" N TYR K 15 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS K 132 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR K 36 " --> pdb=" O LYS K 130 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS K 130 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU K 38 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER K 128 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR K 126 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU K 42 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA K 124 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU K 44 " --> pdb=" O TYR K 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR K 122 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR K 46 " --> pdb=" O SER K 120 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER K 120 " --> pdb=" O TYR K 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 140 through 147 current: chain 'K' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 185 current: chain 'K' and resid 268 through 269 Processing sheet with id=AI3, first strand: chain 'K' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 51 through 54 current: chain 'K' and resid 101 through 110 No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'K' and resid 203 through 204 Processing sheet with id=AI5, first strand: chain 'K' and resid 220 through 221 Processing sheet with id=AI6, first strand: chain 'K' and resid 297 through 306 removed outlier: 5.590A pdb=" N ASP K 298 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS K 321 " --> pdb=" O ASP K 298 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL K 315 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 326 through 329 Processing sheet with id=AI8, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AI9, first strand: chain 'L' and resid 139 through 141 removed outlier: 3.501A pdb=" N VAL L 136 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL L 123 " --> pdb=" O THR L 130 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR L 132 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE L 121 " --> pdb=" O TYR L 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 194 removed outlier: 8.836A pdb=" N ALA L 199 " --> pdb=" O PRO L 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG L 243 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY L 237 " --> pdb=" O GLU L 265 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 222 through 223 removed outlier: 3.885A pdb=" N ALA L 232 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AJ4, first strand: chain 'N' and resid 117 through 119 Processing sheet with id=AJ5, first strand: chain 'O' and resid 117 through 118 968 hydrogen bonds defined for protein. 2472 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: 6.61 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10382 1.34 - 1.46: 7122 1.46 - 1.58: 15327 1.58 - 1.70: 1 1.70 - 1.83: 342 Bond restraints: 33174 Sorted by residual: bond pdb=" CG1 ILE G 143 " pdb=" CD1 ILE G 143 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.12e+00 bond pdb=" CA ASN K 211 " pdb=" C ASN K 211 " ideal model delta sigma weight residual 1.521 1.549 -0.028 1.38e-02 5.25e+03 4.16e+00 bond pdb=" CA LEU B 369 " pdb=" C LEU B 369 " ideal model delta sigma weight residual 1.530 1.553 -0.022 1.12e-02 7.97e+03 4.00e+00 bond pdb=" CB PRO F 174 " pdb=" CG PRO F 174 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.75e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 33169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 44183 2.04 - 4.07: 862 4.07 - 6.11: 91 6.11 - 8.14: 22 8.14 - 10.18: 3 Bond angle restraints: 45161 Sorted by residual: angle pdb=" N LEU K 213 " pdb=" CA LEU K 213 " pdb=" C LEU K 213 " ideal model delta sigma weight residual 111.39 118.47 -7.08 1.38e+00 5.25e-01 2.63e+01 angle pdb=" N ASP K 212 " pdb=" CA ASP K 212 " pdb=" C ASP K 212 " ideal model delta sigma weight residual 111.07 116.29 -5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" N GLU M 117 " pdb=" CA GLU M 117 " pdb=" C GLU M 117 " ideal model delta sigma weight residual 109.07 116.86 -7.79 1.61e+00 3.86e-01 2.34e+01 angle pdb=" CA PRO F 174 " pdb=" N PRO F 174 " pdb=" CD PRO F 174 " ideal model delta sigma weight residual 112.00 105.64 6.36 1.40e+00 5.10e-01 2.06e+01 angle pdb=" N ALA B 372 " pdb=" CA ALA B 372 " pdb=" C ALA B 372 " ideal model delta sigma weight residual 109.72 116.66 -6.94 1.60e+00 3.91e-01 1.88e+01 ... (remaining 45156 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 17987 17.86 - 35.72: 1543 35.72 - 53.58: 251 53.58 - 71.44: 36 71.44 - 89.30: 23 Dihedral angle restraints: 19840 sinusoidal: 7762 harmonic: 12078 Sorted by residual: dihedral pdb=" CB CYS A 153 " pdb=" SG CYS A 153 " pdb=" SG CYS A 265 " pdb=" CB CYS A 265 " ideal model delta sinusoidal sigma weight residual -86.00 0.86 -86.86 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS D 153 " pdb=" SG CYS D 153 " pdb=" SG CYS D 265 " pdb=" CB CYS D 265 " ideal model delta sinusoidal sigma weight residual -86.00 -7.55 -78.45 1 1.00e+01 1.00e-02 7.68e+01 dihedral pdb=" CB CYS K 328 " pdb=" SG CYS K 328 " pdb=" SG CYS K 370 " pdb=" CB CYS K 370 " ideal model delta sinusoidal sigma weight residual 93.00 20.85 72.15 1 1.00e+01 1.00e-02 6.66e+01 ... (remaining 19837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4519 0.083 - 0.165: 510 0.165 - 0.248: 15 0.248 - 0.330: 0 0.330 - 0.413: 2 Chirality restraints: 5046 Sorted by residual: chirality pdb=" C1 NAG H 500 " pdb=" ND2 ASN H 141 " pdb=" C2 NAG H 500 " pdb=" O5 NAG H 500 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG E 500 " pdb=" ND2 ASN E 141 " pdb=" C2 NAG E 500 " pdb=" O5 NAG E 500 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LEU K 213 " pdb=" N LEU K 213 " pdb=" C LEU K 213 " pdb=" CB LEU K 213 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 5043 not shown) Planarity restraints: 5839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 173 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO F 174 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 50 " -0.016 2.00e-02 2.50e+03 2.02e-02 7.17e+00 pdb=" CG PHE G 50 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE G 50 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE G 50 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 50 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE G 50 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE G 50 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 322 " 0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C THR B 322 " -0.045 2.00e-02 2.50e+03 pdb=" O THR B 322 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 323 " 0.015 2.00e-02 2.50e+03 ... (remaining 5836 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2745 2.74 - 3.28: 29997 3.28 - 3.82: 50536 3.82 - 4.36: 60061 4.36 - 4.90: 108317 Nonbonded interactions: 251656 Sorted by model distance: nonbonded pdb=" O SER D 239 " pdb=" OG SER E 57 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN K 43 " pdb=" NE2 HIS K 125 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASN E 325 " pdb=" OG1 THR E 348 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR G 298 " pdb=" O PRO G 303 " model vdw 2.203 3.040 nonbonded pdb=" ND1 HIS L 145 " pdb=" OE2 GLU L 266 " model vdw 2.210 3.120 ... (remaining 251651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.560 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.090 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 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 : 0.008 0.899 33247 Z= 0.369 Angle : 0.808 61.321 45319 Z= 0.427 Chirality : 0.050 0.413 5046 Planarity : 0.005 0.110 5827 Dihedral : 13.158 89.305 11921 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.13), residues: 4151 helix: 1.11 (0.25), residues: 500 sheet: -0.99 (0.14), residues: 1396 loop : -1.84 (0.12), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 229 TYR 0.020 0.002 TYR G 64 PHE 0.045 0.002 PHE G 50 TRP 0.024 0.002 TRP E 89 HIS 0.013 0.001 HIS J 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.24 (33174) covalent geometry : angle 0.69370 / 0.38 (45161) SS BOND : bond 0.13277 / 6.31 ( 61) SS BOND : angle 7.92186 / 5.10 ( 122) hydrogen bonds : bond 0.20586 / 13.99 ( 968) hydrogen bonds : angle 8.24246 / 5.63 ( 2472) link_NAG-ASN : bond 0.00244 / 0.15 ( 12) link_NAG-ASN : angle 2.51116 / 1.60 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 1.240 Fit side-chains revert: symmetry clash REVERT: A 325 MET cc_start: 0.8933 (tmm) cc_final: 0.8359 (tmt) REVERT: E 31 MET cc_start: 0.8827 (ptt) cc_final: 0.8413 (ptt) REVERT: G 325 MET cc_start: 0.8825 (tmm) cc_final: 0.8567 (tmt) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.6488 time to fit residues: 348.7099 Evaluate side-chains 357 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN B 43 ASN C 252 ASN F 197 HIS ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 170 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN H 333 HIS J 170 HIS K 230 HIS O 126 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.127778 restraints weight = 40958.093| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.85 r_work: 0.2854 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 33247 Z= 0.169 Angle : 0.657 13.701 45319 Z= 0.344 Chirality : 0.048 0.392 5046 Planarity : 0.005 0.065 5827 Dihedral : 5.319 29.808 4507 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.66 % Allowed : 9.73 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 4151 helix: 1.03 (0.25), residues: 524 sheet: -0.75 (0.14), residues: 1260 loop : -1.81 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 119 TYR 0.021 0.002 TYR A 199 PHE 0.029 0.002 PHE D 50 TRP 0.012 0.001 TRP L 251 HIS 0.009 0.001 HIS J 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.17 (33174) covalent geometry : angle 0.65144 / 0.34 (45161) SS BOND : bond 0.00462 / 0.26 ( 61) SS BOND : angle 1.30310 / 0.96 ( 122) hydrogen bonds : bond 0.04663 / 3.15 ( 968) hydrogen bonds : angle 6.05845 / 4.15 ( 2472) link_NAG-ASN : bond 0.00367 / 0.22 ( 12) link_NAG-ASN : angle 2.28275 / 1.44 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 392 time to evaluate : 1.153 Fit side-chains REVERT: A 134 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: A 199 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.4969 (t80) REVERT: A 325 MET cc_start: 0.9214 (tmm) cc_final: 0.8505 (tmt) REVERT: D 158 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: E 6 VAL cc_start: 0.8868 (p) cc_final: 0.8638 (t) REVERT: E 31 MET cc_start: 0.9069 (ptt) cc_final: 0.8622 (ptt) REVERT: F 113 MET cc_start: 0.7329 (mpm) cc_final: 0.6815 (mpm) REVERT: F 201 GLN cc_start: 0.7474 (pm20) cc_final: 0.7079 (pm20) REVERT: G 222 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7351 (pp) REVERT: G 325 MET cc_start: 0.9215 (tmm) cc_final: 0.8782 (tmt) REVERT: J 158 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: J 302 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7420 (t0) REVERT: L 111 MET cc_start: 0.5765 (tmm) cc_final: 0.5433 (tmm) REVERT: L 113 MET cc_start: 0.6687 (mpm) cc_final: 0.6465 (mpp) REVERT: L 255 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6407 (mtp) outliers start: 59 outliers final: 28 residues processed: 417 average time/residue: 0.5931 time to fit residues: 296.4665 Evaluate side-chains 398 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 363 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 153 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain G residue 170 HIS Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 302 ASP Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain L residue 255 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 69 optimal weight: 7.9990 chunk 260 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 0.0570 chunk 132 optimal weight: 5.9990 chunk 398 optimal weight: 9.9990 chunk 380 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 43 ASN D 157 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 170 HIS ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS H 325 ASN I 192 HIS J 170 HIS K 139 ASN ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.128276 restraints weight = 40888.660| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.84 r_work: 0.2861 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33247 Z= 0.146 Angle : 0.610 10.382 45319 Z= 0.318 Chirality : 0.046 0.362 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.127 29.362 4507 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.40 % Allowed : 12.44 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.13), residues: 4151 helix: 1.14 (0.25), residues: 524 sheet: -0.62 (0.14), residues: 1312 loop : -1.79 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 119 TYR 0.014 0.002 TYR A 357 PHE 0.025 0.001 PHE D 50 TRP 0.010 0.001 TRP A 329 HIS 0.007 0.001 HIS J 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (33174) covalent geometry : angle 0.60514 / 0.32 (45161) SS BOND : bond 0.00452 / 0.26 ( 61) SS BOND : angle 1.13846 / 0.83 ( 122) hydrogen bonds : bond 0.04000 / 2.70 ( 968) hydrogen bonds : angle 5.62019 / 3.85 ( 2472) link_NAG-ASN : bond 0.00327 / 0.18 ( 12) link_NAG-ASN : angle 2.20272 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 385 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: A 151 ILE cc_start: 0.8863 (mm) cc_final: 0.8581 (mt) REVERT: A 199 TYR cc_start: 0.6046 (OUTLIER) cc_final: 0.4248 (t80) REVERT: A 201 CYS cc_start: 0.7676 (OUTLIER) cc_final: 0.6912 (m) REVERT: A 325 MET cc_start: 0.9213 (tmm) cc_final: 0.8466 (tmt) REVERT: A 326 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: D 45 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8527 (tpp) REVERT: E 6 VAL cc_start: 0.8860 (p) cc_final: 0.8628 (t) REVERT: E 31 MET cc_start: 0.9176 (ptt) cc_final: 0.8689 (ptt) REVERT: F 113 MET cc_start: 0.7495 (mpm) cc_final: 0.7016 (mpm) REVERT: F 201 GLN cc_start: 0.7471 (pm20) cc_final: 0.7054 (pm20) REVERT: G 222 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7359 (pp) REVERT: G 325 MET cc_start: 0.9197 (tmm) cc_final: 0.8862 (tmt) REVERT: I 113 MET cc_start: 0.4665 (OUTLIER) cc_final: 0.4424 (mmt) REVERT: I 255 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5807 (tmm) REVERT: J 158 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: L 240 GLU cc_start: 0.4904 (tp30) cc_final: 0.4196 (tm-30) REVERT: L 255 MET cc_start: 0.7101 (OUTLIER) cc_final: 0.6511 (mtp) REVERT: N 137 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7589 (tm-30) REVERT: N 138 ASN cc_start: 0.7988 (m-40) cc_final: 0.7735 (m110) outliers start: 85 outliers final: 39 residues processed: 418 average time/residue: 0.6226 time to fit residues: 313.7113 Evaluate side-chains 405 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 31 MET Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 390 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 199 optimal weight: 30.0000 chunk 314 optimal weight: 0.9980 chunk 370 optimal weight: 7.9990 chunk 388 optimal weight: 40.0000 chunk 361 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 181 optimal weight: 0.9980 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 252 ASN D 157 GLN E 142 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN G 226 HIS H 43 ASN H 175 ASN J 170 HIS J 232 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121889 restraints weight = 40565.646| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.41 r_work: 0.2881 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 33247 Z= 0.156 Angle : 0.613 9.396 45319 Z= 0.318 Chirality : 0.047 0.352 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.077 29.549 4507 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.24 % Allowed : 14.72 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 4151 helix: 1.46 (0.25), residues: 504 sheet: -0.59 (0.14), residues: 1268 loop : -1.70 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 119 TYR 0.018 0.002 TYR G 199 PHE 0.025 0.001 PHE D 50 TRP 0.018 0.001 TRP L 251 HIS 0.009 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (33174) covalent geometry : angle 0.60706 / 0.32 (45161) SS BOND : bond 0.00498 / 0.31 ( 61) SS BOND : angle 1.23162 / 0.93 ( 122) hydrogen bonds : bond 0.03736 / 2.52 ( 968) hydrogen bonds : angle 5.40086 / 3.71 ( 2472) link_NAG-ASN : bond 0.00265 / 0.15 ( 12) link_NAG-ASN : angle 2.22313 / 1.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 374 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: A 151 ILE cc_start: 0.8891 (mm) cc_final: 0.8593 (mt) REVERT: A 199 TYR cc_start: 0.5739 (OUTLIER) cc_final: 0.4687 (t80) REVERT: A 325 MET cc_start: 0.9223 (tmm) cc_final: 0.8540 (tmt) REVERT: A 326 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: B 2 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8719 (mm-30) REVERT: B 281 ASN cc_start: 0.8757 (t0) cc_final: 0.8433 (t0) REVERT: C 223 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7619 (mp) REVERT: D 45 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8540 (tpp) REVERT: D 76 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7747 (mm-30) REVERT: E 6 VAL cc_start: 0.8882 (p) cc_final: 0.8670 (t) REVERT: E 31 MET cc_start: 0.9111 (ptt) cc_final: 0.8567 (ptt) REVERT: F 113 MET cc_start: 0.7450 (mpm) cc_final: 0.6937 (mpm) REVERT: F 201 GLN cc_start: 0.7413 (pm20) cc_final: 0.6934 (pm20) REVERT: G 222 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7255 (pp) REVERT: G 325 MET cc_start: 0.9169 (tmm) cc_final: 0.8829 (tmt) REVERT: I 255 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5703 (tmm) REVERT: J 158 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: K 433 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7648 (t) REVERT: L 113 MET cc_start: 0.6639 (mpm) cc_final: 0.6195 (mpm) REVERT: L 240 GLU cc_start: 0.4666 (tp30) cc_final: 0.4025 (tm-30) REVERT: L 255 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6292 (mtp) outliers start: 115 outliers final: 60 residues processed: 438 average time/residue: 0.5809 time to fit residues: 306.7450 Evaluate side-chains 429 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 358 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 100 optimal weight: 20.0000 chunk 97 optimal weight: 30.0000 chunk 280 optimal weight: 1.9990 chunk 251 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 396 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS B 43 ASN D 157 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN H 175 ASN J 170 HIS J 232 HIS K 235 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.125776 restraints weight = 40573.375| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.85 r_work: 0.2829 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 33247 Z= 0.228 Angle : 0.676 12.271 45319 Z= 0.351 Chirality : 0.049 0.405 5046 Planarity : 0.005 0.053 5827 Dihedral : 5.323 30.191 4507 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.12 % Allowed : 15.23 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 4151 helix: 1.08 (0.25), residues: 528 sheet: -0.67 (0.14), residues: 1268 loop : -1.76 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 119 TYR 0.018 0.002 TYR J 327 PHE 0.028 0.002 PHE G 50 TRP 0.012 0.002 TRP K 89 HIS 0.012 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.23 (33174) covalent geometry : angle 0.66930 / 0.35 (45161) SS BOND : bond 0.00636 / 0.38 ( 61) SS BOND : angle 1.43427 / 1.06 ( 122) hydrogen bonds : bond 0.04028 / 2.72 ( 968) hydrogen bonds : angle 5.43358 / 3.73 ( 2472) link_NAG-ASN : bond 0.00249 / 0.16 ( 12) link_NAG-ASN : angle 2.43104 / 1.56 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 376 time to evaluate : 1.268 Fit side-chains REVERT: A 134 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7938 (mp10) REVERT: A 151 ILE cc_start: 0.8971 (mm) cc_final: 0.8713 (mt) REVERT: A 199 TYR cc_start: 0.5959 (OUTLIER) cc_final: 0.4087 (t80) REVERT: A 201 CYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6751 (m) REVERT: A 325 MET cc_start: 0.9131 (tmm) cc_final: 0.8574 (tmt) REVERT: A 326 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: B 281 ASN cc_start: 0.8836 (t0) cc_final: 0.8578 (t0) REVERT: D 45 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: D 76 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: D 158 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6788 (mt0) REVERT: E 2 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: E 6 VAL cc_start: 0.8937 (p) cc_final: 0.8710 (t) REVERT: E 31 MET cc_start: 0.9157 (ptt) cc_final: 0.8640 (ptt) REVERT: F 113 MET cc_start: 0.7580 (mpm) cc_final: 0.7083 (mpm) REVERT: F 201 GLN cc_start: 0.7624 (pm20) cc_final: 0.7166 (pm20) REVERT: G 222 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7380 (pp) REVERT: G 256 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8674 (pt) REVERT: G 325 MET cc_start: 0.9152 (tmm) cc_final: 0.8794 (tmt) REVERT: H 75 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8839 (m-30) REVERT: I 255 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.5835 (tmm) REVERT: K 433 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7855 (t) REVERT: L 111 MET cc_start: 0.5501 (tmm) cc_final: 0.5168 (tmm) REVERT: L 113 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6304 (mpm) REVERT: L 240 GLU cc_start: 0.4854 (tp30) cc_final: 0.4237 (tm-30) REVERT: L 255 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6489 (mtp) outliers start: 146 outliers final: 79 residues processed: 464 average time/residue: 0.5895 time to fit residues: 331.9758 Evaluate side-chains 454 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 360 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 45 MET Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 405 THR Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 126 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 286 optimal weight: 20.0000 chunk 309 optimal weight: 0.6980 chunk 168 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 404 optimal weight: 4.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS C 252 ASN D 157 GLN E 142 GLN E 411 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN H 43 ASN J 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128121 restraints weight = 40666.478| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.91 r_work: 0.2868 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33247 Z= 0.117 Angle : 0.586 10.501 45319 Z= 0.305 Chirality : 0.046 0.333 5046 Planarity : 0.004 0.051 5827 Dihedral : 4.973 29.014 4507 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.07 % Allowed : 17.26 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 4151 helix: 1.54 (0.25), residues: 504 sheet: -0.57 (0.14), residues: 1292 loop : -1.63 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 119 TYR 0.017 0.001 TYR G 199 PHE 0.017 0.001 PHE D 50 TRP 0.010 0.001 TRP A 329 HIS 0.006 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (33174) covalent geometry : angle 0.57905 / 0.30 (45161) SS BOND : bond 0.00493 / 0.31 ( 61) SS BOND : angle 1.46581 / 1.12 ( 122) hydrogen bonds : bond 0.03387 / 2.30 ( 968) hydrogen bonds : angle 5.19683 / 3.56 ( 2472) link_NAG-ASN : bond 0.00341 / 0.20 ( 12) link_NAG-ASN : angle 2.17980 / 1.38 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 368 time to evaluate : 1.268 Fit side-chains REVERT: A 134 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7907 (mp10) REVERT: A 151 ILE cc_start: 0.8932 (mm) cc_final: 0.8639 (mt) REVERT: A 199 TYR cc_start: 0.5834 (OUTLIER) cc_final: 0.4163 (t80) REVERT: A 201 CYS cc_start: 0.7818 (OUTLIER) cc_final: 0.6814 (m) REVERT: A 325 MET cc_start: 0.9182 (tmm) cc_final: 0.8529 (tmt) REVERT: A 326 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: B 2 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8698 (mm-30) REVERT: B 281 ASN cc_start: 0.8746 (t0) cc_final: 0.8345 (t0) REVERT: D 76 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: F 113 MET cc_start: 0.7569 (mpm) cc_final: 0.7008 (mpm) REVERT: F 201 GLN cc_start: 0.7519 (pm20) cc_final: 0.7014 (pm20) REVERT: G 222 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7352 (pp) REVERT: G 325 MET cc_start: 0.9153 (tmm) cc_final: 0.8801 (tmt) REVERT: I 255 MET cc_start: 0.6136 (OUTLIER) cc_final: 0.5746 (tmm) REVERT: L 111 MET cc_start: 0.5548 (tmm) cc_final: 0.5195 (tmm) REVERT: L 113 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6220 (mpm) REVERT: L 240 GLU cc_start: 0.4693 (tp30) cc_final: 0.4062 (tm-30) REVERT: L 255 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6318 (mtp) REVERT: M 115 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7389 (pp) outliers start: 109 outliers final: 56 residues processed: 431 average time/residue: 0.6267 time to fit residues: 325.4200 Evaluate side-chains 421 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 217 optimal weight: 0.0050 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 0.0770 chunk 109 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 338 optimal weight: 6.9990 chunk 387 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 212 optimal weight: 4.9990 overall best weight: 2.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN H 175 ASN J 120 ASN J 170 HIS J 184 GLN ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.126685 restraints weight = 40648.835| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.94 r_work: 0.2865 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33247 Z= 0.144 Angle : 0.601 10.131 45319 Z= 0.312 Chirality : 0.046 0.336 5046 Planarity : 0.005 0.050 5827 Dihedral : 4.978 29.127 4507 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.22 % Allowed : 17.83 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.13), residues: 4151 helix: 1.60 (0.25), residues: 504 sheet: -0.53 (0.14), residues: 1292 loop : -1.60 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 119 TYR 0.017 0.002 TYR G 199 PHE 0.020 0.001 PHE D 50 TRP 0.010 0.001 TRP A 329 HIS 0.008 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.14 (33174) covalent geometry : angle 0.59394 / 0.31 (45161) SS BOND : bond 0.00514 / 0.32 ( 61) SS BOND : angle 1.45960 / 1.10 ( 122) hydrogen bonds : bond 0.03453 / 2.34 ( 968) hydrogen bonds : angle 5.13263 / 3.52 ( 2472) link_NAG-ASN : bond 0.00267 / 0.16 ( 12) link_NAG-ASN : angle 2.18072 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 362 time to evaluate : 1.275 Fit side-chains REVERT: A 134 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: A 151 ILE cc_start: 0.8960 (mm) cc_final: 0.8670 (mt) REVERT: A 199 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.4167 (t80) REVERT: A 201 CYS cc_start: 0.7731 (OUTLIER) cc_final: 0.6282 (m) REVERT: A 325 MET cc_start: 0.9201 (tmm) cc_final: 0.8572 (tmt) REVERT: A 326 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: B 2 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 281 ASN cc_start: 0.8768 (t0) cc_final: 0.8401 (t0) REVERT: C 223 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7553 (mp) REVERT: D 76 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7898 (mm-30) REVERT: F 113 MET cc_start: 0.7499 (mpm) cc_final: 0.6954 (mpm) REVERT: F 201 GLN cc_start: 0.7554 (pm20) cc_final: 0.7050 (pm20) REVERT: G 222 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7341 (pp) REVERT: G 325 MET cc_start: 0.9163 (tmm) cc_final: 0.8786 (tmt) REVERT: H 75 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8812 (m-30) REVERT: I 255 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5659 (tmm) REVERT: L 111 MET cc_start: 0.5585 (tmm) cc_final: 0.5221 (tmm) REVERT: L 113 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6209 (mpm) REVERT: L 240 GLU cc_start: 0.4677 (tp30) cc_final: 0.4045 (tm-30) REVERT: L 255 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6323 (mtp) REVERT: M 115 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7358 (pp) outliers start: 114 outliers final: 77 residues processed: 434 average time/residue: 0.6162 time to fit residues: 323.0418 Evaluate side-chains 442 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 353 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain G residue 387 MET Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 112 optimal weight: 6.9990 chunk 301 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 359 optimal weight: 0.0070 chunk 380 optimal weight: 8.9990 chunk 316 optimal weight: 10.0000 chunk 379 optimal weight: 4.9990 chunk 164 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 158 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 HIS A 290 HIS B 43 ASN D 157 GLN E 411 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN H 175 ASN J 170 HIS J 290 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.159109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129950 restraints weight = 40687.261| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.84 r_work: 0.2898 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33247 Z= 0.107 Angle : 0.569 9.967 45319 Z= 0.296 Chirality : 0.045 0.308 5046 Planarity : 0.004 0.050 5827 Dihedral : 4.790 28.408 4507 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.91 % Allowed : 18.70 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4151 helix: 1.67 (0.25), residues: 504 sheet: -0.45 (0.14), residues: 1324 loop : -1.57 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 119 TYR 0.016 0.001 TYR G 199 PHE 0.014 0.001 PHE D 50 TRP 0.009 0.001 TRP A 329 HIS 0.005 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (33174) covalent geometry : angle 0.56330 / 0.29 (45161) SS BOND : bond 0.00361 / 0.23 ( 61) SS BOND : angle 1.19369 / 0.88 ( 122) hydrogen bonds : bond 0.03178 / 2.15 ( 968) hydrogen bonds : angle 5.00440 / 3.43 ( 2472) link_NAG-ASN : bond 0.00321 / 0.18 ( 12) link_NAG-ASN : angle 2.07773 / 1.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 363 time to evaluate : 1.358 Fit side-chains REVERT: A 134 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7889 (mp10) REVERT: A 151 ILE cc_start: 0.8942 (mm) cc_final: 0.8644 (mt) REVERT: A 199 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.4295 (t80) REVERT: A 201 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6594 (m) REVERT: A 325 MET cc_start: 0.9182 (tmm) cc_final: 0.8513 (tmt) REVERT: A 326 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8464 (tt0) REVERT: B 2 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8709 (mm-30) REVERT: B 136 MET cc_start: 0.9243 (mtm) cc_final: 0.8687 (mtm) REVERT: B 281 ASN cc_start: 0.8781 (t0) cc_final: 0.8352 (t0) REVERT: C 223 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7490 (mp) REVERT: D 76 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: E 402 MET cc_start: 0.6922 (mpt) cc_final: 0.6374 (mpt) REVERT: F 113 MET cc_start: 0.7752 (mpm) cc_final: 0.7513 (mmp) REVERT: F 201 GLN cc_start: 0.7526 (pm20) cc_final: 0.7043 (pm20) REVERT: F 252 ASN cc_start: 0.7966 (OUTLIER) cc_final: 0.7417 (t0) REVERT: G 222 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7336 (pp) REVERT: G 325 MET cc_start: 0.9141 (tmm) cc_final: 0.8777 (tmt) REVERT: H 75 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8768 (m-30) REVERT: H 99 GLU cc_start: 0.7679 (mp0) cc_final: 0.7249 (mt-10) REVERT: I 255 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5659 (tmm) REVERT: L 111 MET cc_start: 0.5510 (tmm) cc_final: 0.5152 (tmm) REVERT: L 113 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6317 (mpm) REVERT: L 240 GLU cc_start: 0.4876 (tp30) cc_final: 0.4248 (tm-30) REVERT: L 255 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6260 (mtp) REVERT: M 115 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7262 (pp) outliers start: 103 outliers final: 66 residues processed: 429 average time/residue: 0.6171 time to fit residues: 319.8368 Evaluate side-chains 438 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 359 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain J residue 411 LEU Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 274 optimal weight: 0.0870 chunk 48 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 394 optimal weight: 0.0470 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 HIS A 290 HIS D 157 GLN E 411 GLN F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN H 175 ASN H 394 HIS J 170 HIS J 290 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123528 restraints weight = 40516.393| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.65 r_work: 0.2886 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33247 Z= 0.109 Angle : 0.569 10.057 45319 Z= 0.295 Chirality : 0.045 0.303 5046 Planarity : 0.004 0.050 5827 Dihedral : 4.734 28.058 4507 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.76 % Allowed : 19.10 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.13), residues: 4151 helix: 1.72 (0.25), residues: 504 sheet: -0.39 (0.14), residues: 1264 loop : -1.51 (0.12), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 119 TYR 0.016 0.001 TYR G 199 PHE 0.016 0.001 PHE B 95 TRP 0.009 0.001 TRP A 329 HIS 0.008 0.001 HIS J 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (33174) covalent geometry : angle 0.56344 / 0.29 (45161) SS BOND : bond 0.00435 / 0.26 ( 61) SS BOND : angle 1.15864 / 0.85 ( 122) hydrogen bonds : bond 0.03141 / 2.13 ( 968) hydrogen bonds : angle 4.94366 / 3.39 ( 2472) link_NAG-ASN : bond 0.00291 / 0.17 ( 12) link_NAG-ASN : angle 2.03332 / 1.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 366 time to evaluate : 1.528 Fit side-chains REVERT: A 134 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: A 151 ILE cc_start: 0.8926 (mm) cc_final: 0.8619 (mt) REVERT: A 199 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4213 (t80) REVERT: A 201 CYS cc_start: 0.7750 (OUTLIER) cc_final: 0.6770 (m) REVERT: A 225 CYS cc_start: 0.6104 (OUTLIER) cc_final: 0.4725 (t) REVERT: A 325 MET cc_start: 0.9201 (tmm) cc_final: 0.8542 (tmt) REVERT: A 326 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 2 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 88 MET cc_start: 0.8081 (ttt) cc_final: 0.7857 (ttp) REVERT: B 136 MET cc_start: 0.9238 (mtm) cc_final: 0.8692 (mtm) REVERT: B 281 ASN cc_start: 0.8789 (t0) cc_final: 0.8359 (t0) REVERT: C 183 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8365 (ptmt) REVERT: C 223 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7379 (mp) REVERT: D 76 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: D 289 ASP cc_start: 0.8929 (m-30) cc_final: 0.8698 (m-30) REVERT: E 281 ASN cc_start: 0.7762 (t0) cc_final: 0.7421 (t0) REVERT: F 113 MET cc_start: 0.7738 (mpm) cc_final: 0.7456 (mmp) REVERT: F 201 GLN cc_start: 0.7371 (pm20) cc_final: 0.6791 (pm20) REVERT: F 252 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7383 (t0) REVERT: G 222 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7284 (pp) REVERT: G 325 MET cc_start: 0.9147 (tmm) cc_final: 0.8782 (tmt) REVERT: H 75 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8808 (m-30) REVERT: H 99 GLU cc_start: 0.7753 (mp0) cc_final: 0.7250 (mt-10) REVERT: I 255 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5552 (tmm) REVERT: K 20 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7988 (mt-10) REVERT: K 351 LYS cc_start: 0.8172 (mtmp) cc_final: 0.7921 (mtmm) REVERT: L 111 MET cc_start: 0.5600 (tmm) cc_final: 0.5221 (tmm) REVERT: L 113 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6196 (mpm) REVERT: L 240 GLU cc_start: 0.4519 (tp30) cc_final: 0.3686 (tm-30) REVERT: L 255 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6162 (mtp) REVERT: M 115 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7296 (pp) outliers start: 98 outliers final: 64 residues processed: 430 average time/residue: 0.6224 time to fit residues: 323.0416 Evaluate side-chains 433 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 193 optimal weight: 8.9990 chunk 341 optimal weight: 0.8980 chunk 86 optimal weight: 20.0000 chunk 228 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 300 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 HIS A 290 HIS E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS G 187 ASN H 175 ASN J 170 HIS J 290 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.159895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124118 restraints weight = 40728.711| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.63 r_work: 0.2895 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33247 Z= 0.104 Angle : 0.564 10.257 45319 Z= 0.292 Chirality : 0.045 0.291 5046 Planarity : 0.004 0.050 5827 Dihedral : 4.648 27.639 4507 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.79 % Allowed : 19.21 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4151 helix: 1.75 (0.25), residues: 504 sheet: -0.29 (0.14), residues: 1280 loop : -1.46 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 119 TYR 0.016 0.001 TYR G 199 PHE 0.014 0.001 PHE A 50 TRP 0.009 0.001 TRP A 329 HIS 0.015 0.001 HIS J 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.10 (33174) covalent geometry : angle 0.55990 / 0.29 (45161) SS BOND : bond 0.00385 / 0.23 ( 61) SS BOND : angle 1.09026 / 0.80 ( 122) hydrogen bonds : bond 0.03055 / 2.08 ( 968) hydrogen bonds : angle 4.89405 / 3.36 ( 2472) link_NAG-ASN : bond 0.00297 / 0.17 ( 12) link_NAG-ASN : angle 1.95742 / 1.24 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8302 Ramachandran restraints generated. 4151 Oldfield, 0 Emsley, 4151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 359 time to evaluate : 1.288 Fit side-chains REVERT: A 134 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: A 151 ILE cc_start: 0.8927 (mm) cc_final: 0.8636 (mt) REVERT: A 199 TYR cc_start: 0.5862 (OUTLIER) cc_final: 0.4920 (t80) REVERT: A 325 MET cc_start: 0.9213 (tmm) cc_final: 0.8550 (tmt) REVERT: A 326 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: B 136 MET cc_start: 0.9244 (mtm) cc_final: 0.8693 (mtm) REVERT: B 281 ASN cc_start: 0.8787 (t0) cc_final: 0.8354 (t0) REVERT: D 76 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7829 (mm-30) REVERT: D 215 MET cc_start: 0.6886 (mtp) cc_final: 0.6405 (mpp) REVERT: E 281 ASN cc_start: 0.7826 (t0) cc_final: 0.7499 (t0) REVERT: F 113 MET cc_start: 0.7779 (mpm) cc_final: 0.7478 (mmp) REVERT: F 169 GLU cc_start: 0.7414 (tt0) cc_final: 0.7062 (tt0) REVERT: F 201 GLN cc_start: 0.7355 (pm20) cc_final: 0.6859 (pm20) REVERT: F 252 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7407 (t0) REVERT: G 222 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (pp) REVERT: G 325 MET cc_start: 0.9147 (tmm) cc_final: 0.8779 (tmt) REVERT: H 75 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8796 (m-30) REVERT: H 99 GLU cc_start: 0.7835 (mp0) cc_final: 0.7296 (mt-10) REVERT: I 113 MET cc_start: 0.4557 (OUTLIER) cc_final: 0.4280 (mmt) REVERT: I 255 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5488 (tmm) REVERT: K 20 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7981 (mt-10) REVERT: K 351 LYS cc_start: 0.8191 (mtmp) cc_final: 0.7936 (mtmm) REVERT: L 111 MET cc_start: 0.5584 (tmm) cc_final: 0.5198 (tmm) REVERT: L 113 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6497 (mpm) REVERT: L 240 GLU cc_start: 0.4552 (tp30) cc_final: 0.3735 (tm-30) REVERT: L 255 MET cc_start: 0.7009 (OUTLIER) cc_final: 0.6073 (mtp) REVERT: M 115 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7293 (pp) REVERT: M 133 ARG cc_start: 0.7720 (tmm160) cc_final: 0.7402 (tpm-80) outliers start: 99 outliers final: 67 residues processed: 425 average time/residue: 0.6014 time to fit residues: 308.0585 Evaluate side-chains 428 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 349 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 282 VAL Chi-restraints excluded: chain G residue 290 HIS Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 210 THR Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 301 GLU Chi-restraints excluded: chain J residue 307 GLU Chi-restraints excluded: chain J residue 376 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 183 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 316 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 17 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 264 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 341 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS G 187 ASN H 175 ASN J 170 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.156900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121645 restraints weight = 40701.863| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.51 r_work: 0.2837 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33247 Z= 0.206 Angle : 0.662 10.539 45319 Z= 0.343 Chirality : 0.048 0.353 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.091 28.397 4507 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.85 % Allowed : 19.41 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.13), residues: 4151 helix: 1.66 (0.25), residues: 504 sheet: -0.40 (0.14), residues: 1292 loop : -1.60 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.018 0.002 TYR J 327 PHE 0.022 0.002 PHE A 50 TRP 0.019 0.002 TRP E 89 HIS 0.012 0.001 HIS B 308 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (33174) covalent geometry : angle 0.65562 / 0.34 (45161) SS BOND : bond 0.00637 / 0.37 ( 61) SS BOND : angle 1.48259 / 1.08 ( 122) hydrogen bonds : bond 0.03665 / 2.47 ( 968) hydrogen bonds : angle 5.09511 / 3.49 ( 2472) link_NAG-ASN : bond 0.00182 / 0.11 ( 12) link_NAG-ASN : angle 2.16734 / 1.39 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10387.83 seconds wall clock time: 178 minutes 4.77 seconds (10684.77 seconds total)