Starting phenix.real_space_refine on Fri Jun 27 19:22:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihp_35451/06_2025/8ihp_35451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihp_35451/06_2025/8ihp_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_35451/06_2025/8ihp_35451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihp_35451/06_2025/8ihp_35451.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihp_35451/06_2025/8ihp_35451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihp_35451/06_2025/8ihp_35451.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 17.44, per 1000 atoms: 0.54 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: 6.81 Conformation dependent library (CDL) restraints added in 3.9 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: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.142A pdb=" N PHE A 6 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 350 through 362 Processing helix chain 'A' and resid 362 through 402 Proline residue: A 398 - end of helix removed outlier: 3.518A pdb=" N LEU A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 416 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.883A pdb=" N LYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 259 removed outlier: 3.615A pdb=" N GLY B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 287 removed outlier: 3.630A pdb=" N ALA B 286 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE B 287 " --> pdb=" O ASP B 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 283 through 287' Processing helix chain 'B' and resid 291 through 293 No H-bonds generated for 'chain 'B' and resid 291 through 293' Processing helix chain 'B' and resid 404 through 437 removed outlier: 3.661A pdb=" N TRP B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 437 " --> pdb=" O CYS B 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 116 Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'D' and resid 3 through 8 Processing helix chain 'D' and resid 9 through 12 removed outlier: 3.531A pdb=" N THR D 12 " --> pdb=" O TYR D 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 9 through 12' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.856A pdb=" N LEU D 180 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 181 " --> pdb=" O ARG D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 350 through 360 removed outlier: 3.595A pdb=" N VAL D 355 " --> pdb=" O PRO D 351 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D 356 " --> pdb=" O HIS D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 397 Processing helix chain 'D' and resid 398 through 401 Processing helix chain 'D' and resid 408 through 415 removed outlier: 3.780A pdb=" N LEU D 414 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.562A pdb=" N LYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.688A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 404 through 436 Processing helix chain 'F' and resid 107 through 119 removed outlier: 3.767A pdb=" N MET F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 114 " --> pdb=" O ARG F 110 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.643A pdb=" N MET F 177 " --> pdb=" O PRO F 174 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER F 179 " --> pdb=" O HIS F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 83 No H-bonds generated for 'chain 'G' and resid 81 through 83' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 350 through 360 removed outlier: 3.522A pdb=" N GLN G 356 " --> pdb=" O HIS G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 401 Proline residue: G 398 - end of helix Processing helix chain 'G' and resid 411 through 416 removed outlier: 3.993A pdb=" N CYS G 415 " --> pdb=" O LEU G 411 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS G 416 " --> pdb=" O GLY G 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 411 through 416' Processing helix chain 'H' and resid 238 through 246 removed outlier: 3.568A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.778A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 removed outlier: 3.525A pdb=" N ALA H 286 " --> pdb=" O PRO H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 435 removed outlier: 3.819A pdb=" N TRP H 409 " --> pdb=" O THR H 405 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL H 410 " --> pdb=" O ALA H 406 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 120 removed outlier: 3.794A pdb=" N MET I 113 " --> pdb=" O GLU I 109 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS I 114 " --> pdb=" O ARG I 110 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE I 115 " --> pdb=" O MET I 111 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP I 118 " --> pdb=" O LYS I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 156 Processing helix chain 'I' and resid 174 through 179 removed outlier: 4.112A pdb=" N SER I 179 " --> pdb=" O VAL I 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 11 removed outlier: 3.868A pdb=" N ALA J 11 " --> pdb=" O ASN J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 350 through 360 removed outlier: 3.581A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 397 Processing helix chain 'J' and resid 398 through 400 No H-bonds generated for 'chain 'J' and resid 398 through 400' Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'K' and resid 238 through 247 removed outlier: 3.641A pdb=" N LYS K 245 " --> pdb=" O LYS K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 259 removed outlier: 3.618A pdb=" N GLY K 258 " --> pdb=" O ALA K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 287 Processing helix chain 'K' and resid 289 through 293 Processing helix chain 'K' and resid 404 through 436 removed outlier: 3.573A pdb=" N TRP K 409 " --> pdb=" O THR K 405 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 410 " --> pdb=" O ALA K 406 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.312A pdb=" N GLU L 116 " --> pdb=" O CYS L 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN L 117 " --> pdb=" O MET L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'L' and resid 153 through 157 removed outlier: 3.873A pdb=" N LYS L 157 " --> pdb=" O ASP L 154 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 133 No H-bonds generated for 'chain 'M' and resid 131 through 133' Processing helix chain 'M' and resid 143 through 147 removed outlier: 3.753A pdb=" N GLU M 146 " --> pdb=" O GLY M 143 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU M 147 " --> pdb=" O GLU M 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 143 through 147' Processing helix chain 'N' and resid 131 through 133 No H-bonds generated for 'chain 'N' and resid 131 through 133' Processing helix chain 'O' and resid 131 through 133 No H-bonds generated for 'chain 'O' and resid 131 through 133' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 6.234A pdb=" N LYS A 66 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 156 Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 3.600A pdb=" N VAL A 208 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N CYS A 201 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY A 206 " --> pdb=" O CYS A 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'A' and resid 274 through 277 Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.657A pdb=" N GLN B 160 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.950A pdb=" N LYS B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR B 36 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS B 130 " --> pdb=" O THR B 36 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 38 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER B 128 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 24 through 25 removed outlier: 4.630A pdb=" N THR B 288 " --> pdb=" O SER B 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 42 through 48 removed outlier: 7.013A pdb=" N ALA B 121 " --> pdb=" O GLU B 45 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ILE B 47 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA B 119 " --> pdb=" O ILE B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 100 through 110 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 203 through 204 Processing sheet with id=AB7, first strand: chain 'B' and resid 220 through 221 Processing sheet with id=AB8, first strand: chain 'B' and resid 260 through 261 Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 306 removed outlier: 5.476A pdb=" N ASP B 298 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS B 321 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 315 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 326 through 328 Processing sheet with id=AC2, first strand: chain 'B' and resid 331 through 332 Processing sheet with id=AC3, first strand: chain 'C' and resid 149 through 150 removed outlier: 6.380A pdb=" N PHE C 121 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR C 132 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL C 123 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 130 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N TYR C 132 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 191 through 194 removed outlier: 4.067A pdb=" N GLY C 191 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C 202 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA C 199 " --> pdb=" O PRO C 210 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 210 current: chain 'C' and resid 232 through 238 removed outlier: 7.153A pdb=" N ALA C 232 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TRP C 251 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL C 234 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N VAL C 249 " --> pdb=" O VAL C 234 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 17 through 19 Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 38 removed outlier: 8.328A pdb=" N ILE D 34 " --> pdb=" O SER D 51 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER D 51 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AC8, first strand: chain 'D' and resid 149 through 156 Processing sheet with id=AC9, first strand: chain 'D' and resid 236 through 237 Processing sheet with id=AD1, first strand: chain 'D' and resid 182 through 183 removed outlier: 3.790A pdb=" N MET D 215 " --> pdb=" O ILE D 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AD3, first strand: chain 'D' and resid 274 through 277 Processing sheet with id=AD4, first strand: chain 'D' and resid 306 through 310 removed outlier: 3.504A pdb=" N TYR D 296 " --> pdb=" O HIS D 306 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.668A pdb=" N GLN E 160 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.582A pdb=" N TYR E 15 " --> pdb=" O MET E 31 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 27 through 33 current: chain 'E' and resid 119 through 137 removed outlier: 3.767A pdb=" N TYR E 137 " --> pdb=" O VAL E 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 140 through 147 current: chain 'E' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 184 through 185 current: chain 'E' and resid 268 through 269 Processing sheet with id=AD7, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 100 through 110 No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AD9, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AE1, first strand: chain 'E' and resid 296 through 306 removed outlier: 5.980A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 326 through 329 Processing sheet with id=AE3, first strand: chain 'E' and resid 364 through 367 Processing sheet with id=AE4, first strand: chain 'F' and resid 149 through 150 removed outlier: 6.352A pdb=" N PHE F 121 " --> pdb=" O TYR F 132 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR F 132 " --> pdb=" O PHE F 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL F 123 " --> pdb=" O THR F 130 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N TYR F 132 " --> pdb=" O PRO F 143 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 183 through 184 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 183 through 184 current: chain 'F' and resid 198 through 203 removed outlier: 9.162A pdb=" N ALA F 199 " --> pdb=" O PRO F 210 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN F 201 " --> pdb=" O THR F 208 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 206 through 210 current: chain 'F' and resid 229 through 240 removed outlier: 7.901A pdb=" N ALA F 232 " --> pdb=" O TRP F 251 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N TRP F 251 " --> pdb=" O ALA F 232 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL F 234 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL F 249 " --> pdb=" O VAL F 234 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AE7, first strand: chain 'G' and resid 36 through 38 removed outlier: 9.619A pdb=" N SER G 51 " --> pdb=" O ALA G 70 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA G 70 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS G 66 " --> pdb=" O GLY G 55 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR G 69 " --> pdb=" O GLU G 76 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 84 through 86 Processing sheet with id=AE9, first strand: chain 'G' and resid 149 through 156 Processing sheet with id=AF1, first strand: chain 'G' and resid 236 through 237 Processing sheet with id=AF2, first strand: chain 'G' and resid 175 through 177 removed outlier: 4.612A pdb=" N VAL G 227 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 181 through 182 Processing sheet with id=AF4, first strand: chain 'G' and resid 274 through 277 Processing sheet with id=AF5, first strand: chain 'G' and resid 306 through 310 Processing sheet with id=AF6, first strand: chain 'H' and resid 2 through 8 removed outlier: 3.536A pdb=" N GLN H 160 " --> pdb=" O ASN H 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR H 159 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 15 through 19 removed outlier: 3.716A pdb=" N TYR H 15 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR H 41 " --> pdb=" O HIS H 125 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 137 " --> pdb=" O VAL H 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 140 through 147 current: chain 'H' and resid 184 through 185 Processing sheet with id=AF8, first strand: chain 'H' and resid 24 through 25 removed outlier: 4.678A pdb=" N THR H 288 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 100 through 110 No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AG2, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AG3, first strand: chain 'H' and resid 260 through 262 removed outlier: 4.142A pdb=" N ARG H 267 " --> pdb=" O LYS H 262 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 297 through 306 removed outlier: 4.175A pdb=" N LEU H 299 " --> pdb=" O THR H 319 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR H 319 " --> pdb=" O LEU H 299 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS H 301 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR H 317 " --> pdb=" O CYS H 301 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL H 303 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL H 315 " --> pdb=" O VAL H 303 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AG6, first strand: chain 'I' and resid 128 through 129 removed outlier: 3.559A pdb=" N LYS I 124 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL I 149 " --> pdb=" O LYS I 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 134 through 135 Processing sheet with id=AG8, first strand: chain 'I' and resid 239 through 240 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 239 through 240 current: chain 'I' and resid 199 through 203 removed outlier: 4.144A pdb=" N GLY I 191 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ALA I 232 " --> pdb=" O TRP I 251 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N TRP I 251 " --> pdb=" O ALA I 232 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'J' and resid 37 through 38 removed outlier: 7.167A pdb=" N PHE J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR J 96 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU J 102 " --> pdb=" O HIS J 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 53 through 56 removed outlier: 6.346A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH4, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AH6, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH7, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AH8, first strand: chain 'J' and resid 274 through 278 removed outlier: 4.085A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 306 through 310 Processing sheet with id=AI1, first strand: chain 'K' and resid 2 through 8 Processing sheet with id=AI2, first strand: chain 'K' and resid 15 through 19 removed outlier: 3.509A pdb=" N TYR K 15 " --> pdb=" O MET K 31 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS K 132 " --> pdb=" O VAL K 34 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N THR K 36 " --> pdb=" O LYS K 130 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS K 130 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU K 38 " --> pdb=" O SER K 128 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N SER K 128 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR K 126 " --> pdb=" O PRO K 40 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU K 42 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA K 124 " --> pdb=" O LEU K 42 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU K 44 " --> pdb=" O TYR K 122 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TYR K 122 " --> pdb=" O LEU K 44 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR K 46 " --> pdb=" O SER K 120 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER K 120 " --> pdb=" O TYR K 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 140 through 147 current: chain 'K' and resid 184 through 185 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 184 through 185 current: chain 'K' and resid 268 through 269 Processing sheet with id=AI3, first strand: chain 'K' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 51 through 54 current: chain 'K' and resid 101 through 110 No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'K' and resid 203 through 204 Processing sheet with id=AI5, first strand: chain 'K' and resid 220 through 221 Processing sheet with id=AI6, first strand: chain 'K' and resid 297 through 306 removed outlier: 5.590A pdb=" N ASP K 298 " --> pdb=" O LYS K 321 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS K 321 " --> pdb=" O ASP K 298 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL K 315 " --> pdb=" O ALA K 304 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 326 through 329 Processing sheet with id=AI8, first strand: chain 'K' and resid 331 through 332 Processing sheet with id=AI9, first strand: chain 'L' and resid 139 through 141 removed outlier: 3.501A pdb=" N VAL L 136 " --> pdb=" O LYS L 139 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL L 123 " --> pdb=" O THR L 130 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N TYR L 132 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N PHE L 121 " --> pdb=" O TYR L 132 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'L' and resid 192 through 194 removed outlier: 8.836A pdb=" N ALA L 199 " --> pdb=" O PRO L 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG L 243 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY L 237 " --> pdb=" O GLU L 265 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L' and resid 222 through 223 removed outlier: 3.885A pdb=" N ALA L 232 " --> pdb=" O ILE L 223 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 117 through 119 Processing sheet with id=AJ4, first strand: chain 'N' and resid 117 through 119 Processing sheet with id=AJ5, first strand: chain 'O' and resid 117 through 118 968 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.33 Time building geometry restraints manager: 8.22 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 67.000 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.170 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.360 ------------------------------------------------------------------------------- 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 : 7.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (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 TRP 0.024 0.002 TRP E 89 HIS 0.013 0.001 HIS J 285 PHE 0.045 0.002 PHE G 50 TYR 0.020 0.002 TYR G 64 ARG 0.008 0.001 ARG F 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 12) link_NAG-ASN : angle 2.51116 ( 36) hydrogen bonds : bond 0.20586 ( 968) hydrogen bonds : angle 8.24246 ( 2472) SS BOND : bond 0.13277 ( 61) SS BOND : angle 7.92186 ( 122) covalent geometry : bond 0.00578 (33174) covalent geometry : angle 0.69370 (45161) *********************** 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 : 3.369 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: 1.3638 time to fit residues: 730.9033 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 : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 345 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 209 optimal weight: 0.1980 chunk 165 optimal weight: 3.9990 chunk 320 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 371 optimal weight: 0.0970 overall best weight: 2.4584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 43 ASN H 175 ASN H 333 HIS J 116 GLN J 170 HIS K 230 HIS O 126 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.157145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.127903 restraints weight = 40679.603| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.89 r_work: 0.2867 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33247 Z= 0.144 Angle : 0.636 13.529 45319 Z= 0.334 Chirality : 0.047 0.381 5046 Planarity : 0.005 0.064 5827 Dihedral : 5.923 56.425 4759 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.52 % Allowed : 9.73 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 4151 helix: 1.38 (0.25), residues: 500 sheet: -0.82 (0.14), residues: 1324 loop : -1.73 (0.12), residues: 2327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 251 HIS 0.008 0.001 HIS J 285 PHE 0.026 0.001 PHE D 50 TYR 0.024 0.002 TYR A 199 ARG 0.007 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00424 ( 12) link_NAG-ASN : angle 2.23473 ( 36) hydrogen bonds : bond 0.04468 ( 968) hydrogen bonds : angle 6.02988 ( 2472) SS BOND : bond 0.00391 ( 61) SS BOND : angle 1.24575 ( 122) covalent geometry : bond 0.00341 (33174) covalent geometry : angle 0.63049 (45161) *********************** 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 447 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 393 time to evaluate : 3.620 Fit side-chains REVERT: A 134 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: A 199 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.5031 (t80) REVERT: A 325 MET cc_start: 0.9228 (tmm) cc_final: 0.8460 (tmt) REVERT: A 326 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: E 6 VAL cc_start: 0.8875 (p) cc_final: 0.8661 (t) REVERT: E 31 MET cc_start: 0.9051 (ptt) cc_final: 0.8589 (ptt) REVERT: E 321 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.6532 (ptpp) REVERT: F 113 MET cc_start: 0.7350 (mpm) cc_final: 0.6825 (mpm) REVERT: F 201 GLN cc_start: 0.7455 (pm20) cc_final: 0.7063 (pm20) REVERT: G 222 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7360 (pp) REVERT: G 325 MET cc_start: 0.9180 (tmm) cc_final: 0.8740 (tmt) REVERT: J 158 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7618 (mt0) REVERT: L 111 MET cc_start: 0.5761 (tmm) cc_final: 0.5420 (tmm) REVERT: L 253 LYS cc_start: 0.8016 (tptp) cc_final: 0.7581 (mtmm) REVERT: L 255 MET cc_start: 0.6915 (OUTLIER) cc_final: 0.6493 (mtp) outliers start: 54 outliers final: 25 residues processed: 414 average time/residue: 1.3173 time to fit residues: 653.3828 Evaluate side-chains 394 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 362 time to evaluate : 3.398 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain D residue 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 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 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 22 optimal weight: 9.9990 chunk 382 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 129 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 371 optimal weight: 10.0000 chunk 292 optimal weight: 30.0000 chunk 226 optimal weight: 0.9990 chunk 237 optimal weight: 8.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.156524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127043 restraints weight = 40902.352| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.87 r_work: 0.2850 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33247 Z= 0.185 Angle : 0.642 10.959 45319 Z= 0.334 Chirality : 0.048 0.374 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.811 56.704 4759 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.65 % Allowed : 12.75 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 4151 helix: 1.12 (0.25), residues: 524 sheet: -0.61 (0.14), residues: 1240 loop : -1.78 (0.12), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 251 HIS 0.010 0.001 HIS J 285 PHE 0.030 0.002 PHE G 50 TYR 0.016 0.002 TYR D 327 ARG 0.008 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 12) link_NAG-ASN : angle 2.31882 ( 36) hydrogen bonds : bond 0.04179 ( 968) hydrogen bonds : angle 5.65010 ( 2472) SS BOND : bond 0.00557 ( 61) SS BOND : angle 1.22658 ( 122) covalent geometry : bond 0.00463 (33174) covalent geometry : angle 0.63612 (45161) *********************** 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 479 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 385 time to evaluate : 3.271 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: A 151 ILE cc_start: 0.8898 (mm) cc_final: 0.8618 (mt) REVERT: A 199 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.4131 (t80) REVERT: A 201 CYS cc_start: 0.7671 (OUTLIER) cc_final: 0.6802 (m) REVERT: A 325 MET cc_start: 0.9198 (tmm) cc_final: 0.8495 (tmt) REVERT: C 223 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7805 (mp) REVERT: D 45 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8562 (tpp) REVERT: E 6 VAL cc_start: 0.8891 (p) cc_final: 0.8639 (t) REVERT: E 31 MET cc_start: 0.9161 (ptt) cc_final: 0.8671 (ptt) REVERT: F 113 MET cc_start: 0.7554 (mpm) cc_final: 0.7073 (mpm) REVERT: F 201 GLN cc_start: 0.7517 (pm20) cc_final: 0.7124 (pm20) REVERT: G 222 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7397 (pp) REVERT: G 325 MET cc_start: 0.9200 (tmm) cc_final: 0.8873 (tmt) REVERT: J 158 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: K 292 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: L 240 GLU cc_start: 0.4984 (tp30) cc_final: 0.4315 (tm-30) REVERT: L 255 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6534 (mtp) REVERT: N 137 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7605 (tm-30) REVERT: N 138 ASN cc_start: 0.8007 (m-40) cc_final: 0.7757 (m110) outliers start: 94 outliers final: 46 residues processed: 429 average time/residue: 1.2756 time to fit residues: 657.5973 Evaluate side-chains 412 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 357 time to evaluate : 3.529 ------------------------------------------------------------------------------- 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 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 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 223 ILE 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 76 GLU 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 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 J residue 158 GLN Chi-restraints excluded: chain J residue 180 LEU 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 269 MET Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 292 GLU 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 203 optimal weight: 1.9990 chunk 324 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 219 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 397 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 358 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 142 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN G 120 ASN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 HIS H 175 ASN J 170 HIS J 232 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119419 restraints weight = 40467.734| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.69 r_work: 0.2855 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 33247 Z= 0.192 Angle : 0.646 9.423 45319 Z= 0.336 Chirality : 0.048 0.383 5046 Planarity : 0.005 0.052 5827 Dihedral : 5.745 56.769 4759 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.44 % Allowed : 14.72 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.13), residues: 4151 helix: 1.08 (0.25), residues: 528 sheet: -0.62 (0.14), residues: 1248 loop : -1.77 (0.12), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP L 251 HIS 0.010 0.001 HIS B 308 PHE 0.027 0.002 PHE D 50 TYR 0.018 0.002 TYR G 199 ARG 0.008 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 2.38433 ( 36) hydrogen bonds : bond 0.03949 ( 968) hydrogen bonds : angle 5.48987 ( 2472) SS BOND : bond 0.00581 ( 61) SS BOND : angle 1.33624 ( 122) covalent geometry : bond 0.00480 (33174) covalent geometry : angle 0.64025 (45161) *********************** 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 495 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 373 time to evaluate : 3.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: A 151 ILE cc_start: 0.8933 (mm) cc_final: 0.8648 (mt) REVERT: A 199 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.4774 (t80) REVERT: A 325 MET cc_start: 0.9202 (tmm) cc_final: 0.8592 (tmt) REVERT: A 326 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: C 223 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7586 (mp) REVERT: D 45 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: D 158 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: E 2 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: E 6 VAL cc_start: 0.8898 (p) cc_final: 0.8665 (t) REVERT: E 31 MET cc_start: 0.9171 (ptt) cc_final: 0.8716 (ptt) REVERT: F 113 MET cc_start: 0.7506 (mpm) cc_final: 0.6964 (mpm) REVERT: F 201 GLN cc_start: 0.7477 (pm20) cc_final: 0.7011 (pm20) REVERT: G 222 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7279 (pp) REVERT: G 325 MET cc_start: 0.9173 (tmm) cc_final: 0.8827 (tmt) REVERT: K 292 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: K 433 CYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7685 (t) REVERT: L 111 MET cc_start: 0.5784 (tmm) cc_final: 0.5515 (tmm) REVERT: L 113 MET cc_start: 0.6453 (mpm) cc_final: 0.6249 (mpp) REVERT: L 240 GLU cc_start: 0.4691 (tp30) cc_final: 0.4070 (tm-30) REVERT: L 255 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6414 (mtp) outliers start: 122 outliers final: 67 residues processed: 443 average time/residue: 1.2863 time to fit residues: 688.5025 Evaluate side-chains 433 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 355 time to evaluate : 3.238 ------------------------------------------------------------------------------- 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 281 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain B residue 433 CYS Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 TRP Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 45 MET Chi-restraints excluded: chain D residue 76 GLU Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 199 TYR Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 2 GLU 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 402 MET Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 42 THR 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 351 LYS 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 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 31 MET 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 213 LEU 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 292 GLU 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 76 optimal weight: 1.9990 chunk 224 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 339 optimal weight: 9.9990 chunk 296 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 379 optimal weight: 0.6980 chunk 372 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 43 ASN J 170 HIS J 232 HIS K 235 GLN N 138 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.130562 restraints weight = 40702.581| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.80 r_work: 0.2909 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 33247 Z= 0.100 Angle : 0.555 10.328 45319 Z= 0.288 Chirality : 0.045 0.307 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.206 55.924 4759 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.40 % Allowed : 16.42 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4151 helix: 1.57 (0.25), residues: 504 sheet: -0.50 (0.14), residues: 1324 loop : -1.59 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 329 HIS 0.004 0.001 HIS F 145 PHE 0.014 0.001 PHE D 50 TYR 0.016 0.001 TYR G 199 ARG 0.010 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 12) link_NAG-ASN : angle 2.07080 ( 36) hydrogen bonds : bond 0.03242 ( 968) hydrogen bonds : angle 5.15775 ( 2472) SS BOND : bond 0.00438 ( 61) SS BOND : angle 1.21475 ( 122) covalent geometry : bond 0.00231 (33174) covalent geometry : angle 0.54896 (45161) *********************** 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 460 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 375 time to evaluate : 3.464 Fit side-chains revert: symmetry clash REVERT: A 134 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7801 (mp10) REVERT: A 151 ILE cc_start: 0.8882 (mm) cc_final: 0.8576 (mt) REVERT: A 166 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8323 (pm20) REVERT: A 199 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.4050 (t80) REVERT: A 201 CYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6616 (m) REVERT: A 325 MET cc_start: 0.9194 (tmm) cc_final: 0.8481 (tmt) REVERT: A 326 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: B 136 MET cc_start: 0.9212 (mtm) cc_final: 0.8670 (mtm) REVERT: B 281 ASN cc_start: 0.8620 (t0) cc_final: 0.8404 (t0) REVERT: C 223 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7554 (mp) REVERT: E 281 ASN cc_start: 0.7806 (t0) cc_final: 0.7587 (t0) REVERT: F 113 MET cc_start: 0.7825 (mpm) cc_final: 0.7309 (mpm) REVERT: F 201 GLN cc_start: 0.7492 (pm20) cc_final: 0.7038 (pm20) REVERT: G 222 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7438 (pp) REVERT: G 325 MET cc_start: 0.9162 (tmm) cc_final: 0.8796 (tmt) REVERT: H 75 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: I 113 MET cc_start: 0.4672 (OUTLIER) cc_final: 0.4397 (mmt) REVERT: I 250 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7596 (p) REVERT: K 292 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: L 111 MET cc_start: 0.5261 (tmm) cc_final: 0.4967 (tmm) REVERT: L 113 MET cc_start: 0.6663 (mpm) cc_final: 0.6226 (mpm) REVERT: L 240 GLU cc_start: 0.4955 (tp30) cc_final: 0.4338 (tm-30) REVERT: L 255 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6354 (mtp) outliers start: 85 outliers final: 38 residues processed: 424 average time/residue: 1.1979 time to fit residues: 615.2139 Evaluate side-chains 406 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 356 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL 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 223 ILE 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 D residue 393 SER Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 199 TYR Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP 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 113 MET Chi-restraints excluded: chain I residue 250 THR 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 47 ILE Chi-restraints excluded: chain K residue 140 VAL Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 292 GLU Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain M residue 125 THR 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 286 optimal weight: 40.0000 chunk 256 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 263 optimal weight: 0.1980 chunk 206 optimal weight: 8.9990 chunk 214 optimal weight: 1.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 J 170 HIS J 290 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.157076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.121756 restraints weight = 40676.211| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 3.50 r_work: 0.2855 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 33247 Z= 0.179 Angle : 0.623 10.359 45319 Z= 0.323 Chirality : 0.047 0.349 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.409 56.762 4759 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.41 % Allowed : 17.04 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4151 helix: 1.58 (0.25), residues: 504 sheet: -0.52 (0.14), residues: 1284 loop : -1.61 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 329 HIS 0.010 0.001 HIS B 308 PHE 0.024 0.002 PHE D 50 TYR 0.018 0.002 TYR J 327 ARG 0.009 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 2.20584 ( 36) hydrogen bonds : bond 0.03623 ( 968) hydrogen bonds : angle 5.18493 ( 2472) SS BOND : bond 0.00584 ( 61) SS BOND : angle 1.44739 ( 122) covalent geometry : bond 0.00453 (33174) covalent geometry : angle 0.61659 (45161) *********************** 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 485 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 364 time to evaluate : 3.458 Fit side-chains REVERT: A 90 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8068 (m-30) REVERT: A 134 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7982 (mp10) REVERT: A 151 ILE cc_start: 0.8952 (mm) cc_final: 0.8648 (mt) REVERT: A 199 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.4280 (t80) REVERT: A 201 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.6934 (m) REVERT: A 225 CYS cc_start: 0.6390 (OUTLIER) cc_final: 0.5222 (t) REVERT: A 325 MET cc_start: 0.9213 (tmm) cc_final: 0.8585 (tmt) REVERT: B 95 PHE cc_start: 0.8530 (t80) cc_final: 0.8262 (t80) REVERT: B 281 ASN cc_start: 0.8691 (t0) cc_final: 0.8476 (t0) REVERT: C 223 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7508 (mp) REVERT: E 281 ASN cc_start: 0.7885 (t0) cc_final: 0.7639 (t0) REVERT: F 113 MET cc_start: 0.7566 (mpm) cc_final: 0.6961 (mpm) REVERT: F 201 GLN cc_start: 0.7491 (pm20) cc_final: 0.6987 (pm20) REVERT: G 222 ILE cc_start: 0.7575 (OUTLIER) cc_final: 0.7301 (pp) REVERT: G 325 MET cc_start: 0.9189 (tmm) cc_final: 0.8812 (tmt) REVERT: H 75 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8858 (m-30) REVERT: H 213 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8124 (tm) REVERT: K 292 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: L 111 MET cc_start: 0.5476 (tmm) cc_final: 0.5232 (tmm) REVERT: L 113 MET cc_start: 0.6498 (OUTLIER) cc_final: 0.6186 (mpp) REVERT: L 240 GLU cc_start: 0.4530 (tp30) cc_final: 0.3955 (tm-30) REVERT: L 255 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6308 (mtp) REVERT: M 115 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7467 (pp) outliers start: 121 outliers final: 69 residues processed: 437 average time/residue: 1.2727 time to fit residues: 673.9026 Evaluate side-chains 436 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 354 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP 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 90 ASP Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 199 TYR 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 300 THR 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 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 H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 213 LEU 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 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 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 31 MET 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 285 SER Chi-restraints excluded: chain K residue 288 THR Chi-restraints excluded: chain K residue 292 GLU Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 128 ILE 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 118 optimal weight: 5.9990 chunk 347 optimal weight: 30.0000 chunk 173 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 124 optimal weight: 4.9990 chunk 349 optimal weight: 9.9990 chunk 257 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 247 optimal weight: 30.0000 chunk 176 optimal weight: 5.9990 chunk 274 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 290 HIS B 43 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN H 175 ASN H 325 ASN J 170 HIS J 184 GLN J 290 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.156393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119578 restraints weight = 40656.550| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.70 r_work: 0.2851 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33247 Z= 0.206 Angle : 0.653 10.812 45319 Z= 0.340 Chirality : 0.048 0.374 5046 Planarity : 0.005 0.051 5827 Dihedral : 5.580 56.936 4759 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.78 % Allowed : 17.35 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 4151 helix: 1.54 (0.25), residues: 504 sheet: -0.51 (0.14), residues: 1268 loop : -1.67 (0.12), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 89 HIS 0.017 0.001 HIS J 290 PHE 0.023 0.002 PHE D 50 TYR 0.017 0.002 TYR G 199 ARG 0.009 0.001 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 2.32484 ( 36) hydrogen bonds : bond 0.03760 ( 968) hydrogen bonds : angle 5.22871 ( 2472) SS BOND : bond 0.00616 ( 61) SS BOND : angle 1.77751 ( 122) covalent geometry : bond 0.00518 (33174) covalent geometry : angle 0.64473 (45161) *********************** 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 496 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 362 time to evaluate : 3.567 Fit side-chains REVERT: A 90 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: A 134 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: A 151 ILE cc_start: 0.8981 (mm) cc_final: 0.8705 (mt) REVERT: A 199 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.4211 (t80) REVERT: A 201 CYS cc_start: 0.7721 (OUTLIER) cc_final: 0.6876 (m) REVERT: A 225 CYS cc_start: 0.6413 (OUTLIER) cc_final: 0.5032 (t) REVERT: A 325 MET cc_start: 0.9197 (tmm) cc_final: 0.8639 (tmt) REVERT: B 95 PHE cc_start: 0.8179 (t80) cc_final: 0.7943 (t80) REVERT: B 281 ASN cc_start: 0.8712 (t0) cc_final: 0.8431 (t0) REVERT: E 2 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7328 (mp0) REVERT: E 281 ASN cc_start: 0.7800 (t0) cc_final: 0.7384 (t0) REVERT: F 113 MET cc_start: 0.7457 (mpm) cc_final: 0.6844 (mpm) REVERT: F 169 GLU cc_start: 0.7418 (tt0) cc_final: 0.7062 (tt0) REVERT: F 201 GLN cc_start: 0.7533 (pm20) cc_final: 0.7013 (pm20) REVERT: G 222 ILE cc_start: 0.7569 (OUTLIER) cc_final: 0.7287 (pp) REVERT: G 325 MET cc_start: 0.9169 (tmm) cc_final: 0.8795 (tmt) REVERT: H 75 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8835 (m-30) REVERT: H 213 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8090 (tm) REVERT: I 250 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7396 (p) REVERT: J 48 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8394 (mp) REVERT: K 292 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: L 113 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.6136 (mpp) REVERT: L 240 GLU cc_start: 0.4439 (tp30) cc_final: 0.3881 (tm-30) REVERT: L 255 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6323 (mtp) REVERT: M 115 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7385 (pp) outliers start: 134 outliers final: 87 residues processed: 443 average time/residue: 1.2167 time to fit residues: 653.1497 Evaluate side-chains 452 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 350 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP 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 90 ASP Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 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 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 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 D residue 199 TYR 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 280 MET Chi-restraints excluded: chain E residue 282 LEU 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 E residue 402 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 255 MET 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 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 213 LEU 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 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 292 GLU Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 128 ILE 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 111 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 276 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 326 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 303 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 368 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 255 HIS A 290 HIS B 100 ASN ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 411 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 ASN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 120 ASN G 187 ASN H 43 ASN H 175 ASN H 325 ASN J 170 HIS J 290 HIS N 138 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.128938 restraints weight = 40583.563| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.85 r_work: 0.2877 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33247 Z= 0.120 Angle : 0.588 10.063 45319 Z= 0.305 Chirality : 0.045 0.328 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.301 56.186 4759 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.93 % Allowed : 18.73 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4151 helix: 1.63 (0.25), residues: 504 sheet: -0.50 (0.14), residues: 1316 loop : -1.61 (0.12), residues: 2331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 329 HIS 0.021 0.001 HIS J 290 PHE 0.016 0.001 PHE D 50 TYR 0.017 0.001 TYR G 199 ARG 0.009 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 12) link_NAG-ASN : angle 2.17567 ( 36) hydrogen bonds : bond 0.03330 ( 968) hydrogen bonds : angle 5.08186 ( 2472) SS BOND : bond 0.00436 ( 61) SS BOND : angle 1.36740 ( 122) covalent geometry : bond 0.00288 (33174) covalent geometry : angle 0.58116 (45161) *********************** 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 468 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 364 time to evaluate : 3.769 Fit side-chains REVERT: A 90 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: A 134 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: A 151 ILE cc_start: 0.8974 (mm) cc_final: 0.8686 (mt) REVERT: A 199 TYR cc_start: 0.5992 (OUTLIER) cc_final: 0.4419 (t80) REVERT: A 201 CYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6791 (m) REVERT: A 225 CYS cc_start: 0.6272 (OUTLIER) cc_final: 0.4891 (t) REVERT: A 325 MET cc_start: 0.9173 (tmm) cc_final: 0.8546 (tmt) REVERT: B 95 PHE cc_start: 0.8063 (t80) cc_final: 0.7859 (t80) REVERT: B 136 MET cc_start: 0.9213 (mtm) cc_final: 0.8683 (mtm) REVERT: E 2 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7240 (mp0) REVERT: E 281 ASN cc_start: 0.7765 (t0) cc_final: 0.7357 (t0) REVERT: F 113 MET cc_start: 0.7769 (mpm) cc_final: 0.7169 (mpm) REVERT: F 169 GLU cc_start: 0.7479 (tt0) cc_final: 0.7203 (tt0) REVERT: F 201 GLN cc_start: 0.7598 (pm20) cc_final: 0.7101 (pm20) REVERT: F 252 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7490 (t0) REVERT: G 222 ILE cc_start: 0.7658 (OUTLIER) cc_final: 0.7381 (pp) REVERT: G 325 MET cc_start: 0.9145 (tmm) cc_final: 0.8783 (tmt) REVERT: H 75 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8756 (m-30) REVERT: J 158 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7605 (mt0) REVERT: K 292 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: L 111 MET cc_start: 0.5591 (tmm) cc_final: 0.5276 (tmm) REVERT: L 113 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6253 (mpm) REVERT: L 240 GLU cc_start: 0.4748 (tp30) cc_final: 0.4171 (tm-30) REVERT: L 255 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6371 (mtp) REVERT: M 115 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7288 (pp) outliers start: 104 outliers final: 66 residues processed: 428 average time/residue: 1.3000 time to fit residues: 673.7733 Evaluate side-chains 437 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 357 time to evaluate : 3.462 ------------------------------------------------------------------------------- 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 90 ASP Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 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 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 199 TYR Chi-restraints excluded: chain D residue 393 SER Chi-restraints excluded: chain E residue 2 GLU 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 321 LYS Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 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 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 351 LYS Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain H residue 425 ILE Chi-restraints excluded: chain I residue 147 LYS Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN 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 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 292 GLU 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 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 202 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 407 optimal weight: 20.0000 chunk 277 optimal weight: 6.9990 chunk 320 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 389 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 HIS A 290 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN H 175 ASN J 170 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.122638 restraints weight = 40596.118| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.43 r_work: 0.2858 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33247 Z= 0.151 Angle : 0.612 9.801 45319 Z= 0.317 Chirality : 0.046 0.340 5046 Planarity : 0.005 0.050 5827 Dihedral : 5.347 56.515 4759 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.02 % Allowed : 19.07 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 4151 helix: 1.33 (0.25), residues: 528 sheet: -0.44 (0.14), residues: 1272 loop : -1.62 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 89 HIS 0.009 0.001 HIS B 308 PHE 0.020 0.001 PHE D 50 TYR 0.017 0.002 TYR G 199 ARG 0.009 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00262 ( 12) link_NAG-ASN : angle 2.22220 ( 36) hydrogen bonds : bond 0.03457 ( 968) hydrogen bonds : angle 5.07007 ( 2472) SS BOND : bond 0.00479 ( 61) SS BOND : angle 1.34172 ( 122) covalent geometry : bond 0.00373 (33174) covalent geometry : angle 0.60627 (45161) *********************** 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 467 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 360 time to evaluate : 3.456 Fit side-chains REVERT: A 90 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: A 134 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7895 (mp10) REVERT: A 151 ILE cc_start: 0.8957 (mm) cc_final: 0.8666 (mt) REVERT: A 199 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.4255 (t80) REVERT: A 201 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6882 (m) REVERT: A 225 CYS cc_start: 0.6164 (OUTLIER) cc_final: 0.4806 (t) REVERT: A 325 MET cc_start: 0.9234 (tmm) cc_final: 0.8643 (tmt) REVERT: B 88 MET cc_start: 0.8133 (ttt) cc_final: 0.7891 (ttp) REVERT: B 136 MET cc_start: 0.9249 (mtm) cc_final: 0.8713 (mtm) REVERT: D 76 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: E 2 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: E 281 ASN cc_start: 0.7763 (t0) cc_final: 0.7348 (t0) REVERT: E 402 MET cc_start: 0.6866 (mpt) cc_final: 0.6214 (mpt) REVERT: F 113 MET cc_start: 0.7694 (mpm) cc_final: 0.7038 (mpm) REVERT: F 169 GLU cc_start: 0.7399 (tt0) cc_final: 0.7086 (tt0) REVERT: F 201 GLN cc_start: 0.7412 (pm20) cc_final: 0.6897 (pm20) REVERT: F 252 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7364 (t0) REVERT: G 222 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7240 (pp) REVERT: G 325 MET cc_start: 0.9186 (tmm) cc_final: 0.8822 (tmt) REVERT: H 75 ASP cc_start: 0.9083 (OUTLIER) cc_final: 0.8815 (m-30) REVERT: J 158 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7602 (mt0) REVERT: K 292 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: L 111 MET cc_start: 0.5822 (tmm) cc_final: 0.5497 (tmm) REVERT: L 113 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.6085 (mpm) REVERT: L 240 GLU cc_start: 0.4397 (tp30) cc_final: 0.3596 (tm-30) REVERT: L 255 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6288 (mtp) REVERT: M 115 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7292 (pp) outliers start: 107 outliers final: 74 residues processed: 431 average time/residue: 1.2636 time to fit residues: 658.5218 Evaluate side-chains 442 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 353 time to evaluate : 3.254 ------------------------------------------------------------------------------- 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 90 ASP Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 225 CYS Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 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 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 76 GLU Chi-restraints excluded: chain D residue 199 TYR 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 160 GLN 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 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 259 VAL 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 H residue 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 305 THR Chi-restraints excluded: chain H residue 307 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 147 LYS Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN 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 183 GLU Chi-restraints excluded: chain K residue 231 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 292 GLU 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 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 118 optimal weight: 4.9990 chunk 245 optimal weight: 1.9990 chunk 312 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 356 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 C 252 ASN D 157 GLN E 411 GLN ** G 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 ASN H 175 ASN J 170 HIS J 290 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.159395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.126902 restraints weight = 40483.422| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 3.26 r_work: 0.2876 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33247 Z= 0.109 Angle : 0.576 10.780 45319 Z= 0.297 Chirality : 0.045 0.304 5046 Planarity : 0.004 0.050 5827 Dihedral : 5.094 55.817 4759 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.51 % Allowed : 19.46 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.13), residues: 4151 helix: 1.72 (0.25), residues: 504 sheet: -0.33 (0.14), residues: 1284 loop : -1.51 (0.12), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 329 HIS 0.006 0.001 HIS B 308 PHE 0.019 0.001 PHE G 100 TYR 0.016 0.001 TYR G 199 ARG 0.010 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 12) link_NAG-ASN : angle 2.10711 ( 36) hydrogen bonds : bond 0.03138 ( 968) hydrogen bonds : angle 4.96021 ( 2472) SS BOND : bond 0.00401 ( 61) SS BOND : angle 1.20136 ( 122) covalent geometry : bond 0.00259 (33174) covalent geometry : angle 0.57031 (45161) ********************** 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 450 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 361 time to evaluate : 3.701 Fit side-chains REVERT: A 134 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7885 (mp10) REVERT: A 151 ILE cc_start: 0.8935 (mm) cc_final: 0.8627 (mt) REVERT: A 199 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.4946 (t80) REVERT: A 325 MET cc_start: 0.9222 (tmm) cc_final: 0.8588 (tmt) REVERT: B 136 MET cc_start: 0.9240 (mtm) cc_final: 0.8689 (mtm) REVERT: E 281 ASN cc_start: 0.7722 (t0) cc_final: 0.7412 (t0) REVERT: F 113 MET cc_start: 0.7755 (mpm) cc_final: 0.7440 (mmp) REVERT: F 169 GLU cc_start: 0.7385 (tt0) cc_final: 0.7046 (tt0) REVERT: F 201 GLN cc_start: 0.7391 (pm20) cc_final: 0.6849 (pm20) REVERT: F 252 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7341 (t0) REVERT: G 222 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7275 (pp) REVERT: G 325 MET cc_start: 0.9183 (tmm) cc_final: 0.8815 (tmt) REVERT: J 158 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: K 292 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: L 111 MET cc_start: 0.5843 (tmm) cc_final: 0.5549 (tmm) REVERT: L 113 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6061 (mpm) REVERT: L 240 GLU cc_start: 0.4371 (tp30) cc_final: 0.3567 (tm-30) REVERT: L 255 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6220 (mtp) REVERT: M 115 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7214 (pp) REVERT: M 133 ARG cc_start: 0.7644 (tmm160) cc_final: 0.7300 (tpm-80) outliers start: 89 outliers final: 65 residues processed: 422 average time/residue: 1.2932 time to fit residues: 662.4564 Evaluate side-chains 425 residues out of total 3545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 351 time to evaluate : 3.355 ------------------------------------------------------------------------------- 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 272 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 433 CYS 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 199 TYR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 160 GLN Chi-restraints excluded: chain E residue 280 MET Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 252 ASN Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 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 36 THR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 307 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 147 LYS Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 158 GLN 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 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 292 GLU Chi-restraints excluded: chain K residue 339 LEU Chi-restraints excluded: chain K residue 433 CYS Chi-restraints excluded: chain L residue 113 MET Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 208 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 125 THR Chi-restraints excluded: chain O residue 139 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 409 random chunks: chunk 332 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 398 optimal weight: 20.0000 chunk 268 optimal weight: 3.9990 chunk 247 optimal weight: 50.0000 chunk 141 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 278 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 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 J 290 HIS ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.156786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.114783 restraints weight = 40640.917| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.65 r_work: 0.3019 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33247 Z= 0.143 Angle : 0.604 10.575 45319 Z= 0.312 Chirality : 0.046 0.324 5046 Planarity : 0.005 0.053 5827 Dihedral : 5.216 56.310 4759 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.76 % Allowed : 19.32 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4151 helix: 1.73 (0.25), residues: 504 sheet: -0.36 (0.14), residues: 1300 loop : -1.56 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 89 HIS 0.008 0.001 HIS B 308 PHE 0.019 0.001 PHE D 50 TYR 0.016 0.001 TYR G 199 ARG 0.009 0.000 ARG D 119 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 12) link_NAG-ASN : angle 2.12102 ( 36) hydrogen bonds : bond 0.03325 ( 968) hydrogen bonds : angle 4.99013 ( 2472) SS BOND : bond 0.00484 ( 61) SS BOND : angle 1.41327 ( 122) covalent geometry : bond 0.00353 (33174) covalent geometry : angle 0.59779 (45161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23482.66 seconds wall clock time: 405 minutes 5.65 seconds (24305.65 seconds total)