Starting phenix.real_space_refine on Fri Mar 6 15:28:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihp_35451/03_2026/8ihp_35451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihp_35451/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihp_35451/03_2026/8ihp_35451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihp_35451/03_2026/8ihp_35451.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihp_35451/03_2026/8ihp_35451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihp_35451/03_2026/8ihp_35451.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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 dihedrals: 6 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 dihedrals: 3 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: 7.14, 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 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: 1.27 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: 6.56 Time building geometry restraints manager: 3.17 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: 18207 17.86 - 35.72: 1555 35.72 - 53.58: 267 53.58 - 71.44: 40 71.44 - 89.30: 23 Dihedral angle restraints: 20092 sinusoidal: 8014 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 20089 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: 0.01 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: 3.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.810 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 : 13.201 89.305 12173 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 covalent geometry : bond 0.00578 (33174) covalent geometry : angle 0.69370 (45161) SS BOND : bond 0.13277 ( 61) SS BOND : angle 7.92186 ( 122) hydrogen bonds : bond 0.20586 ( 968) hydrogen bonds : angle 8.24246 ( 2472) link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 2.51116 ( 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 : 1.261 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: 0.6517 time to fit residues: 348.4388 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 : 1.183 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.156832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.127605 restraints weight = 40961.170| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.86 r_work: 0.2847 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33247 Z= 0.170 Angle : 0.657 13.685 45319 Z= 0.344 Chirality : 0.048 0.400 5046 Planarity : 0.005 0.065 5827 Dihedral : 6.026 56.799 4759 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.61 % Allowed : 9.73 % Favored : 88.66 % 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: -1.63 (0.13), residues: 4151 helix: 1.02 (0.25), residues: 524 sheet: -0.75 (0.14), residues: 1260 loop : -1.82 (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 0.013 0.001 TRP L 251 HIS 0.009 0.001 HIS J 285 Details of bonding type rmsd covalent geometry : bond 0.00417 (33174) covalent geometry : angle 0.65174 (45161) SS BOND : bond 0.00480 ( 61) SS BOND : angle 1.31085 ( 122) hydrogen bonds : bond 0.04703 ( 968) hydrogen bonds : angle 6.07236 ( 2472) link_NAG-ASN : bond 0.00387 ( 12) link_NAG-ASN : angle 2.30714 ( 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 449 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 392 time to evaluate : 0.966 Fit side-chains REVERT: A 134 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8065 (mp10) REVERT: A 199 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4992 (t80) REVERT: A 325 MET cc_start: 0.9248 (tmm) cc_final: 0.8539 (tmt) REVERT: D 158 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.6971 (mt0) REVERT: E 6 VAL cc_start: 0.8891 (p) cc_final: 0.8657 (t) REVERT: E 31 MET cc_start: 0.9064 (ptt) cc_final: 0.8611 (ptt) REVERT: E 321 LYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6560 (ptpp) REVERT: F 113 MET cc_start: 0.7285 (mpm) cc_final: 0.6825 (mpm) REVERT: F 201 GLN cc_start: 0.7472 (pm20) cc_final: 0.7071 (pm20) REVERT: G 222 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7339 (pp) REVERT: G 325 MET cc_start: 0.9216 (tmm) cc_final: 0.8785 (tmt) REVERT: J 158 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: J 302 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7406 (t0) REVERT: L 111 MET cc_start: 0.5796 (tmm) cc_final: 0.5432 (tmm) REVERT: L 113 MET cc_start: 0.6560 (mpm) cc_final: 0.6313 (mpp) REVERT: L 255 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6404 (mtp) outliers start: 57 outliers final: 28 residues processed: 416 average time/residue: 0.6190 time to fit residues: 307.4867 Evaluate side-chains 400 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 364 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 5 THR 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 E residue 321 LYS 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 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: 4.9990 chunk 260 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 108 optimal weight: 0.0170 chunk 132 optimal weight: 5.9990 chunk 398 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 405 optimal weight: 4.9990 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3781 r_free = 0.3781 target = 0.156818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127756 restraints weight = 40878.839| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.82 r_work: 0.2853 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1102 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= 0.166 Angle : 0.629 10.607 45319 Z= 0.328 Chirality : 0.047 0.368 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.797 56.538 4759 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.68 % Allowed : 12.61 % Favored : 84.71 % 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: -1.55 (0.13), residues: 4151 helix: 1.12 (0.25), residues: 524 sheet: -0.63 (0.14), residues: 1264 loop : -1.81 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 119 TYR 0.015 0.002 TYR A 357 PHE 0.026 0.002 PHE G 50 TRP 0.011 0.001 TRP L 251 HIS 0.009 0.001 HIS J 285 Details of bonding type rmsd covalent geometry : bond 0.00412 (33174) covalent geometry : angle 0.62334 (45161) SS BOND : bond 0.00444 ( 61) SS BOND : angle 1.20345 ( 122) hydrogen bonds : bond 0.04118 ( 968) hydrogen bonds : angle 5.65620 ( 2472) link_NAG-ASN : bond 0.00337 ( 12) link_NAG-ASN : angle 2.28930 ( 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 480 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 385 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 151 ILE cc_start: 0.8884 (mm) cc_final: 0.8606 (mt) REVERT: A 199 TYR cc_start: 0.6068 (OUTLIER) cc_final: 0.4185 (t80) REVERT: A 201 CYS cc_start: 0.7686 (OUTLIER) cc_final: 0.6832 (m) REVERT: A 325 MET cc_start: 0.9238 (tmm) cc_final: 0.8536 (tmt) REVERT: D 45 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: D 158 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6844 (mt0) REVERT: E 6 VAL cc_start: 0.8875 (p) cc_final: 0.8628 (t) REVERT: E 31 MET cc_start: 0.9158 (ptt) cc_final: 0.8665 (ptt) REVERT: F 113 MET cc_start: 0.7518 (mpm) cc_final: 0.7037 (mpm) REVERT: F 201 GLN cc_start: 0.7497 (pm20) cc_final: 0.7095 (pm20) REVERT: G 222 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7363 (pp) REVERT: G 325 MET cc_start: 0.9213 (tmm) cc_final: 0.8888 (tmt) REVERT: I 113 MET cc_start: 0.4682 (OUTLIER) cc_final: 0.4464 (mmt) REVERT: I 255 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5800 (tmm) REVERT: J 158 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7610 (mt0) REVERT: L 240 GLU cc_start: 0.4915 (tp30) cc_final: 0.4208 (tm-30) REVERT: L 255 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6500 (mtp) REVERT: N 137 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7612 (tm-30) REVERT: N 138 ASN cc_start: 0.7992 (m-40) cc_final: 0.7750 (m110) outliers start: 95 outliers final: 42 residues processed: 422 average time/residue: 0.6407 time to fit residues: 323.7777 Evaluate side-chains 413 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 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 158 GLN Chi-restraints excluded: chain D residue 199 TYR 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 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 231 VAL 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: 8.9990 chunk 180 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 199 optimal weight: 30.0000 chunk 314 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 388 optimal weight: 40.0000 chunk 361 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS 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 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 = 0.3778 r_free = 0.3778 target = 0.156620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120076 restraints weight = 40583.525| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.73 r_work: 0.2853 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33247 Z= 0.171 Angle : 0.628 9.425 45319 Z= 0.326 Chirality : 0.047 0.369 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.664 56.629 4759 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.50 % Allowed : 14.53 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.50 (0.13), residues: 4151 helix: 1.10 (0.25), residues: 528 sheet: -0.61 (0.14), residues: 1248 loop : -1.76 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 119 TYR 0.018 0.002 TYR G 199 PHE 0.026 0.002 PHE D 50 TRP 0.019 0.001 TRP L 251 HIS 0.009 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00425 (33174) covalent geometry : angle 0.62200 (45161) SS BOND : bond 0.00559 ( 61) SS BOND : angle 1.28720 ( 122) hydrogen bonds : bond 0.03836 ( 968) hydrogen bonds : angle 5.44699 ( 2472) link_NAG-ASN : bond 0.00281 ( 12) link_NAG-ASN : angle 2.32416 ( 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 498 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 374 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: A 151 ILE cc_start: 0.8918 (mm) cc_final: 0.8634 (mt) REVERT: A 199 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4728 (t80) REVERT: A 325 MET cc_start: 0.9211 (tmm) cc_final: 0.8594 (tmt) REVERT: B 2 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8760 (mm-30) REVERT: B 281 ASN cc_start: 0.8780 (t0) cc_final: 0.8463 (t0) REVERT: C 223 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7489 (mp) REVERT: D 45 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8572 (tpp) REVERT: D 76 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7963 (mm-30) REVERT: E 6 VAL cc_start: 0.8870 (p) cc_final: 0.8646 (t) REVERT: E 31 MET cc_start: 0.9169 (ptt) cc_final: 0.8726 (ptt) REVERT: F 113 MET cc_start: 0.7398 (mpm) cc_final: 0.6872 (mpm) REVERT: F 201 GLN cc_start: 0.7400 (pm20) cc_final: 0.6919 (pm20) REVERT: G 222 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7218 (pp) REVERT: G 325 MET cc_start: 0.9174 (tmm) cc_final: 0.8826 (tmt) REVERT: I 255 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.5824 (tmm) REVERT: K 433 CYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7591 (t) REVERT: L 111 MET cc_start: 0.5760 (tmm) cc_final: 0.5492 (tmm) REVERT: L 113 MET cc_start: 0.6588 (mpm) cc_final: 0.6262 (mpt) REVERT: L 240 GLU cc_start: 0.4557 (tp30) cc_final: 0.3913 (tm-30) REVERT: L 255 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6312 (mtp) outliers start: 124 outliers final: 59 residues processed: 444 average time/residue: 0.6196 time to fit residues: 330.5578 Evaluate side-chains 420 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 352 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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: 8.9990 chunk 251 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 396 optimal weight: 0.0670 chunk 86 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3764 r_free = 0.3764 target = 0.155331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.118972 restraints weight = 40675.090| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.62 r_work: 0.2834 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1278 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= 0.229 Angle : 0.680 12.638 45319 Z= 0.354 Chirality : 0.049 0.406 5046 Planarity : 0.005 0.054 5827 Dihedral : 5.821 57.143 4759 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.06 % Allowed : 15.54 % Favored : 80.39 % 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: -1.59 (0.13), residues: 4151 helix: 1.08 (0.25), residues: 528 sheet: -0.70 (0.14), residues: 1276 loop : -1.83 (0.12), residues: 2347 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 0.027 0.002 PHE D 50 TRP 0.013 0.002 TRP K 89 HIS 0.012 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00579 (33174) covalent geometry : angle 0.67355 (45161) SS BOND : bond 0.00584 ( 61) SS BOND : angle 1.41765 ( 122) hydrogen bonds : bond 0.04063 ( 968) hydrogen bonds : angle 5.44990 ( 2472) link_NAG-ASN : bond 0.00263 ( 12) link_NAG-ASN : angle 2.49414 ( 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: 144 poor density : 378 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: A 151 ILE cc_start: 0.8963 (mm) cc_final: 0.8705 (mt) REVERT: A 199 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.3959 (t80) REVERT: A 201 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6681 (m) REVERT: A 325 MET cc_start: 0.9183 (tmm) cc_final: 0.8635 (tmt) REVERT: B 281 ASN cc_start: 0.8830 (t0) cc_final: 0.8552 (t0) REVERT: B 371 SER cc_start: 0.7428 (m) cc_final: 0.6742 (p) REVERT: D 45 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8579 (tpp) REVERT: E 2 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: E 6 VAL cc_start: 0.8927 (p) cc_final: 0.8696 (t) REVERT: F 113 MET cc_start: 0.7496 (mpm) cc_final: 0.6941 (mpm) REVERT: F 201 GLN cc_start: 0.7534 (pm20) cc_final: 0.7034 (pm20) REVERT: G 222 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7248 (pp) REVERT: G 325 MET cc_start: 0.9190 (tmm) cc_final: 0.8839 (tmt) REVERT: H 75 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8893 (m-30) REVERT: I 255 MET cc_start: 0.6257 (OUTLIER) cc_final: 0.5728 (tmm) REVERT: K 99 GLU cc_start: 0.7922 (mp0) cc_final: 0.7664 (mp0) REVERT: K 433 CYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7710 (t) REVERT: L 111 MET cc_start: 0.5787 (tmm) cc_final: 0.5443 (tmm) REVERT: L 240 GLU cc_start: 0.4506 (tp30) cc_final: 0.3901 (tm-30) REVERT: L 255 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6413 (mtp) outliers start: 144 outliers final: 85 residues processed: 465 average time/residue: 0.6106 time to fit residues: 341.6316 Evaluate side-chains 458 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 363 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 5 THR 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 302 THR 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 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 282 LEU 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 42 THR 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 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 208 VAL 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 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 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 401 ASP Chi-restraints excluded: chain K residue 433 CYS 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: 0.9990 chunk 286 optimal weight: 20.0000 chunk 309 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 280 optimal weight: 7.9990 chunk 327 optimal weight: 8.9990 chunk 355 optimal weight: 9.9990 chunk 404 optimal weight: 40.0000 chunk 31 optimal weight: 0.4980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS C 252 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** F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN G 290 HIS H 175 ASN J 170 HIS J 232 HIS M 116 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.121980 restraints weight = 40650.603| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.52 r_work: 0.2868 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33247 Z= 0.129 Angle : 0.600 10.964 45319 Z= 0.312 Chirality : 0.046 0.351 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.471 56.255 4759 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.36 % Allowed : 16.95 % Favored : 79.69 % 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: -1.42 (0.13), residues: 4151 helix: 1.19 (0.25), residues: 528 sheet: -0.59 (0.14), residues: 1272 loop : -1.70 (0.12), residues: 2351 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 0.018 0.001 PHE D 50 TRP 0.011 0.001 TRP A 329 HIS 0.007 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00312 (33174) covalent geometry : angle 0.59252 (45161) SS BOND : bond 0.00521 ( 61) SS BOND : angle 1.53481 ( 122) hydrogen bonds : bond 0.03483 ( 968) hydrogen bonds : angle 5.24113 ( 2472) link_NAG-ASN : bond 0.00326 ( 12) link_NAG-ASN : angle 2.27287 ( 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 489 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 370 time to evaluate : 1.267 Fit side-chains REVERT: A 134 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: A 151 ILE cc_start: 0.8937 (mm) cc_final: 0.8643 (mt) REVERT: A 199 TYR cc_start: 0.5810 (OUTLIER) cc_final: 0.4099 (t80) REVERT: A 201 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6626 (m) REVERT: A 325 MET cc_start: 0.9203 (tmm) cc_final: 0.8612 (tmt) REVERT: B 281 ASN cc_start: 0.8737 (t0) cc_final: 0.8415 (t0) REVERT: D 76 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7857 (mm-30) REVERT: F 113 MET cc_start: 0.7584 (mpm) cc_final: 0.6995 (mpm) REVERT: F 201 GLN cc_start: 0.7462 (pm20) cc_final: 0.6940 (pm20) REVERT: G 222 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7287 (pp) REVERT: G 325 MET cc_start: 0.9166 (tmm) cc_final: 0.8807 (tmt) REVERT: H 75 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8788 (m-30) REVERT: I 250 THR cc_start: 0.7697 (OUTLIER) cc_final: 0.7479 (p) REVERT: I 255 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5726 (tmm) REVERT: J 48 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8363 (mp) REVERT: L 111 MET cc_start: 0.5518 (tmm) cc_final: 0.5200 (tmm) REVERT: L 113 MET cc_start: 0.6492 (mpm) cc_final: 0.6196 (mpp) REVERT: L 240 GLU cc_start: 0.4524 (tp30) cc_final: 0.3914 (tm-30) REVERT: L 255 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6283 (mtp) REVERT: M 115 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7353 (pp) outliers start: 119 outliers final: 62 residues processed: 440 average time/residue: 0.6338 time to fit residues: 335.5428 Evaluate side-chains 430 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 357 time to evaluate : 1.232 ------------------------------------------------------------------------------- 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 233 LYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP 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 200 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET 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 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 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 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 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 48 ILE Chi-restraints excluded: chain J residue 50 PHE 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 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 401 ASP 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: 2.9990 chunk 20 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 338 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 212 optimal weight: 0.0040 overall best weight: 4.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS D 157 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN G 290 HIS H 175 ASN H 325 ASN J 120 ASN J 170 HIS J 184 GLN J 290 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.119075 restraints weight = 40626.193| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.73 r_work: 0.2847 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1441 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= 0.207 Angle : 0.659 10.966 45319 Z= 0.342 Chirality : 0.048 0.380 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.657 57.003 4759 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.67 % Allowed : 17.66 % Favored : 78.67 % 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: -1.44 (0.13), residues: 4151 helix: 1.18 (0.25), residues: 528 sheet: -0.59 (0.14), residues: 1268 loop : -1.72 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 119 TYR 0.017 0.002 TYR G 199 PHE 0.023 0.002 PHE D 50 TRP 0.017 0.002 TRP E 89 HIS 0.011 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00519 (33174) covalent geometry : angle 0.65122 (45161) SS BOND : bond 0.00631 ( 61) SS BOND : angle 1.59460 ( 122) hydrogen bonds : bond 0.03817 ( 968) hydrogen bonds : angle 5.27113 ( 2472) link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 2.40810 ( 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 497 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 367 time to evaluate : 1.259 Fit side-chains REVERT: A 134 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7876 (mp10) REVERT: A 151 ILE cc_start: 0.8976 (mm) cc_final: 0.8702 (mt) REVERT: A 199 TYR cc_start: 0.5890 (OUTLIER) cc_final: 0.4113 (t80) REVERT: A 201 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.6427 (m) REVERT: A 280 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7957 (mpt180) REVERT: A 325 MET cc_start: 0.9166 (tmm) cc_final: 0.8619 (tmt) REVERT: D 76 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: E 2 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: F 113 MET cc_start: 0.7561 (mpm) cc_final: 0.6954 (mpm) REVERT: F 201 GLN cc_start: 0.7451 (pm20) cc_final: 0.6944 (pm20) REVERT: G 222 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7280 (pp) REVERT: G 325 MET cc_start: 0.9169 (tmm) cc_final: 0.8808 (tmt) REVERT: H 75 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: I 250 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7448 (p) REVERT: I 255 MET cc_start: 0.6203 (OUTLIER) cc_final: 0.5739 (tmm) REVERT: J 48 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (mp) REVERT: L 240 GLU cc_start: 0.4429 (tp30) cc_final: 0.3821 (tm-30) REVERT: L 255 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6409 (mtp) REVERT: M 115 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7343 (pp) outliers start: 130 outliers final: 92 residues processed: 451 average time/residue: 0.6155 time to fit residues: 334.3270 Evaluate side-chains 460 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 355 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 280 ARG Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 318 ILE 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 34 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 351 LYS Chi-restraints excluded: chain B residue 385 ASP 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 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 318 ILE Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain D residue 407 VAL 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 146 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 208 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 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 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 302 THR 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 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 48 ILE 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 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 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 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 251 TRP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 112 optimal weight: 7.9990 chunk 301 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 359 optimal weight: 0.0670 chunk 380 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 379 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS B 43 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 G 290 HIS H 43 ASN H 175 ASN H 325 ASN J 120 ASN J 170 HIS J 290 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.159240 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 = 40698.904| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.84 r_work: 0.2899 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33247 Z= 0.100 Angle : 0.573 10.238 45319 Z= 0.298 Chirality : 0.045 0.308 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.223 55.803 4759 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.37 % Allowed : 19.35 % Favored : 78.28 % 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: -1.22 (0.13), residues: 4151 helix: 1.62 (0.25), residues: 504 sheet: -0.49 (0.14), residues: 1324 loop : -1.60 (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 0.016 0.001 PHE G 100 TRP 0.011 0.001 TRP G 329 HIS 0.025 0.001 HIS J 290 Details of bonding type rmsd covalent geometry : bond 0.00229 (33174) covalent geometry : angle 0.56727 (45161) SS BOND : bond 0.00383 ( 61) SS BOND : angle 1.22059 ( 122) hydrogen bonds : bond 0.03163 ( 968) hydrogen bonds : angle 5.05718 ( 2472) link_NAG-ASN : bond 0.00376 ( 12) link_NAG-ASN : angle 2.18927 ( 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 453 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 369 time to evaluate : 1.236 Fit side-chains REVERT: A 134 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7871 (mp10) REVERT: A 151 ILE cc_start: 0.8930 (mm) cc_final: 0.8633 (mt) REVERT: A 166 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: A 199 TYR cc_start: 0.5976 (OUTLIER) cc_final: 0.5040 (t80) REVERT: A 325 MET cc_start: 0.9158 (tmm) cc_final: 0.8572 (tmt) REVERT: B 136 MET cc_start: 0.9231 (mtm) cc_final: 0.8677 (mtm) REVERT: E 402 MET cc_start: 0.6922 (mpt) cc_final: 0.6371 (mpt) REVERT: F 113 MET cc_start: 0.7733 (mpm) cc_final: 0.7141 (mpm) REVERT: F 201 GLN cc_start: 0.7466 (pm20) cc_final: 0.6964 (pm20) REVERT: F 252 ASN cc_start: 0.7934 (m-40) cc_final: 0.7397 (t0) REVERT: G 222 ILE cc_start: 0.7619 (OUTLIER) cc_final: 0.7355 (pp) REVERT: G 325 MET cc_start: 0.9128 (tmm) cc_final: 0.8764 (tmt) REVERT: I 113 MET cc_start: 0.4602 (OUTLIER) cc_final: 0.4306 (mmt) REVERT: I 255 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5647 (tmm) REVERT: L 111 MET cc_start: 0.5624 (tmm) cc_final: 0.5350 (tmm) REVERT: L 113 MET cc_start: 0.6482 (mpm) cc_final: 0.6051 (mpm) REVERT: L 240 GLU cc_start: 0.4751 (tp30) cc_final: 0.4135 (tm-30) REVERT: L 255 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6281 (mtp) REVERT: M 115 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7260 (pp) outliers start: 84 outliers final: 49 residues processed: 424 average time/residue: 0.6252 time to fit residues: 318.3907 Evaluate side-chains 408 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 210 THR 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 297 ILE 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 199 TYR Chi-restraints excluded: chain E residue 36 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 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 302 THR Chi-restraints excluded: chain H residue 307 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 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 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 K residue 433 CYS 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 M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 372 optimal weight: 5.9990 chunk 234 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 338 optimal weight: 0.7980 chunk 394 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN G 290 HIS H 175 ASN J 170 HIS K 142 GLN ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.157947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128891 restraints weight = 40550.735| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.82 r_work: 0.2877 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33247 Z= 0.142 Angle : 0.606 10.187 45319 Z= 0.313 Chirality : 0.046 0.326 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.284 56.352 4759 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.45 % Allowed : 19.80 % 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: -1.21 (0.13), residues: 4151 helix: 1.66 (0.25), residues: 504 sheet: -0.45 (0.14), residues: 1316 loop : -1.63 (0.12), residues: 2331 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 0.018 0.001 PHE D 50 TRP 0.011 0.001 TRP E 89 HIS 0.008 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00351 (33174) covalent geometry : angle 0.59968 (45161) SS BOND : bond 0.00499 ( 61) SS BOND : angle 1.38410 ( 122) hydrogen bonds : bond 0.03351 ( 968) hydrogen bonds : angle 5.04733 ( 2472) link_NAG-ASN : bond 0.00264 ( 12) link_NAG-ASN : angle 2.19987 ( 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 441 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 354 time to evaluate : 1.299 Fit side-chains REVERT: A 134 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 151 ILE cc_start: 0.8957 (mm) cc_final: 0.8674 (mt) REVERT: A 199 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.4634 (t80) REVERT: A 201 CYS cc_start: 0.7540 (OUTLIER) cc_final: 0.6699 (m) REVERT: A 325 MET cc_start: 0.9156 (tmm) cc_final: 0.8564 (tmt) REVERT: B 88 MET cc_start: 0.8102 (ttt) cc_final: 0.7844 (ttp) REVERT: B 136 MET cc_start: 0.9236 (mtm) cc_final: 0.8698 (mtm) REVERT: C 183 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8453 (ptmt) REVERT: D 45 MET cc_start: 0.8793 (ttm) cc_final: 0.8590 (tpp) REVERT: F 113 MET cc_start: 0.7762 (mpm) cc_final: 0.7178 (mpm) REVERT: F 201 GLN cc_start: 0.7536 (pm20) cc_final: 0.7063 (pm20) REVERT: F 229 ARG cc_start: 0.6946 (mtm110) cc_final: 0.6742 (mtm110) REVERT: F 252 ASN cc_start: 0.8020 (m-40) cc_final: 0.7498 (t0) REVERT: G 222 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7363 (pp) REVERT: G 325 MET cc_start: 0.9147 (tmm) cc_final: 0.8768 (tmt) REVERT: H 75 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8796 (m-30) REVERT: I 120 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7421 (mm) REVERT: I 255 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5734 (tmm) REVERT: K 99 GLU cc_start: 0.7895 (mp0) cc_final: 0.7629 (mp0) REVERT: L 111 MET cc_start: 0.5385 (tmm) cc_final: 0.5119 (tmm) REVERT: L 113 MET cc_start: 0.6608 (mpm) cc_final: 0.6348 (mpp) REVERT: L 240 GLU cc_start: 0.4862 (tp30) cc_final: 0.4272 (tm-30) REVERT: L 255 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6429 (mtp) REVERT: M 115 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7216 (pp) outliers start: 87 outliers final: 68 residues processed: 415 average time/residue: 0.6336 time to fit residues: 316.2677 Evaluate side-chains 428 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 351 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 272 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 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 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 C residue 257 THR Chi-restraints excluded: chain D residue 40 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 146 VAL 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 255 MET 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 36 THR 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 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE 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 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 339 LEU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 433 CYS 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 M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR 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: 7.9990 chunk 228 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 186 optimal weight: 9.9990 chunk 229 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS C 252 ASN D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS G 187 ASN G 290 HIS H 175 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 = 0.3805 r_free = 0.3805 target = 0.158896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.129646 restraints weight = 40734.401| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.84 r_work: 0.2887 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1739 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= 0.114 Angle : 0.586 10.184 45319 Z= 0.303 Chirality : 0.045 0.311 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.174 55.991 4759 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.68 % Allowed : 19.72 % Favored : 77.60 % 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: -1.15 (0.13), residues: 4151 helix: 1.70 (0.25), residues: 504 sheet: -0.41 (0.14), residues: 1324 loop : -1.59 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 289 TYR 0.016 0.001 TYR G 199 PHE 0.016 0.001 PHE A 50 TRP 0.012 0.001 TRP L 251 HIS 0.019 0.001 HIS G 290 Details of bonding type rmsd covalent geometry : bond 0.00272 (33174) covalent geometry : angle 0.58050 (45161) SS BOND : bond 0.00423 ( 61) SS BOND : angle 1.25422 ( 122) hydrogen bonds : bond 0.03191 ( 968) hydrogen bonds : angle 4.99635 ( 2472) link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.14632 ( 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 455 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 360 time to evaluate : 1.300 Fit side-chains REVERT: A 134 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: A 151 ILE cc_start: 0.8952 (mm) cc_final: 0.8666 (mt) REVERT: A 199 TYR cc_start: 0.5943 (OUTLIER) cc_final: 0.4766 (t80) REVERT: A 201 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6594 (m) REVERT: A 325 MET cc_start: 0.9176 (tmm) cc_final: 0.8592 (tmt) REVERT: B 88 MET cc_start: 0.8063 (ttt) cc_final: 0.7839 (ttp) REVERT: B 136 MET cc_start: 0.9247 (mtm) cc_final: 0.8719 (mtm) REVERT: F 113 MET cc_start: 0.7762 (mpm) cc_final: 0.7512 (mmp) REVERT: F 201 GLN cc_start: 0.7519 (pm20) cc_final: 0.6988 (pm20) REVERT: F 252 ASN cc_start: 0.7973 (m-40) cc_final: 0.7452 (t0) REVERT: G 222 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7394 (pp) REVERT: G 325 MET cc_start: 0.9163 (tmm) cc_final: 0.8776 (tmt) REVERT: H 75 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8792 (m-30) REVERT: I 120 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7428 (mm) REVERT: I 255 MET cc_start: 0.6032 (OUTLIER) cc_final: 0.5673 (tmm) REVERT: K 99 GLU cc_start: 0.7928 (mp0) cc_final: 0.7634 (mp0) REVERT: L 113 MET cc_start: 0.6603 (mpm) cc_final: 0.6369 (mpp) REVERT: L 240 GLU cc_start: 0.4844 (tp30) cc_final: 0.4014 (tm-30) REVERT: L 255 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6363 (mtp) REVERT: M 115 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7209 (pp) REVERT: M 133 ARG cc_start: 0.7800 (tmm160) cc_final: 0.7505 (tpm-80) outliers start: 95 outliers final: 63 residues processed: 427 average time/residue: 0.6327 time to fit residues: 324.5164 Evaluate side-chains 426 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 354 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 210 THR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 31 MET 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 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 234 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 280 MET 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 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 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 302 THR Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 255 MET Chi-restraints excluded: chain J residue 50 PHE 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 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 K residue 401 ASP Chi-restraints excluded: chain K residue 433 CYS 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 M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 316 optimal weight: 6.9990 chunk 191 optimal weight: 40.0000 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 264 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 276 optimal weight: 20.0000 chunk 131 optimal weight: 0.9980 chunk 341 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS E 411 GLN F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS G 187 ASN G 290 HIS H 175 ASN J 170 HIS ** 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 = 0.3778 r_free = 0.3778 target = 0.156665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.123178 restraints weight = 40783.015| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 3.26 r_work: 0.2856 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33247 Z= 0.191 Angle : 0.650 10.731 45319 Z= 0.336 Chirality : 0.048 0.361 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.489 56.958 4759 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 2.85 % Allowed : 19.63 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.22 (0.13), residues: 4151 helix: 1.63 (0.25), residues: 504 sheet: -0.44 (0.14), residues: 1292 loop : -1.63 (0.12), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 119 TYR 0.017 0.002 TYR G 199 PHE 0.022 0.002 PHE A 50 TRP 0.019 0.001 TRP E 89 HIS 0.011 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00478 (33174) covalent geometry : angle 0.64332 (45161) SS BOND : bond 0.00586 ( 61) SS BOND : angle 1.43856 ( 122) hydrogen bonds : bond 0.03619 ( 968) hydrogen bonds : angle 5.11477 ( 2472) link_NAG-ASN : bond 0.00224 ( 12) link_NAG-ASN : angle 2.29519 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10580.42 seconds wall clock time: 181 minutes 13.32 seconds (10873.32 seconds total)