Starting phenix.real_space_refine on Mon Jul 6 20:28:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cte_26988/07_2026/8cte_26988.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.083 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 P 6 5.49 5 S 174 5.16 5 C 25336 2.51 5 N 6491 2.21 5 O 6837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38844 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3431 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "X" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5167 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 6339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6339 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6406 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 768} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "O" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "R" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "M" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P1L:plan-1': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 43 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.47 residue: pdb=" N AARG S 234 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG S 234 " occ=0.52 residue: pdb=" N AARG O 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG O 234 " occ=0.50 residue: pdb=" N AARG R 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG R 234 " occ=0.50 residue: pdb=" N AARG M 234 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG M 234 " occ=0.49 Time building chain proxies: 9.18, per 1000 atoms: 0.24 Number of scatterers: 38844 At special positions: 0 Unit cell: (137.78, 182.6, 201.69, 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) S 174 16.00 P 6 15.00 O 6837 8.00 N 6491 7.00 C 25336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 P1002 " - " ASN P 642 " " NAG T1002 " - " ASN T 642 " Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 2.1 seconds 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9180 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 23 sheets defined 63.9% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 23 Processing helix chain 'A' and resid 24 through 35 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 90 through 100 Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.510A pdb=" N GLU A 121 " --> pdb=" O MET A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 156 through 167 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.563A pdb=" N ILE A 212 " --> pdb=" O THR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 Processing helix chain 'A' and resid 241 through 250 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 274 through 283 removed outlier: 3.526A pdb=" N ASN A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 317 through 327 Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 350 through 360 Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 449 through 460 Processing helix chain 'W' and resid 4 through 7 Processing helix chain 'W' and resid 8 through 17 Processing helix chain 'W' and resid 18 through 22 Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.659A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 160 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 4.167A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 257 removed outlier: 4.067A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.263A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 374 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.680A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.808A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 43 through 65 removed outlier: 3.886A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 99 removed outlier: 3.651A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 128 removed outlier: 3.536A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 162 Processing helix chain 'K' and resid 165 through 170 removed outlier: 3.745A pdb=" N LEU K 169 " --> pdb=" O HIS K 166 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 187 Processing helix chain 'K' and resid 202 through 225 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 230 through 256 Processing helix chain 'K' and resid 266 through 274 removed outlier: 3.511A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 290 through 312 removed outlier: 3.680A pdb=" N ALA K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 326 through 350 removed outlier: 3.660A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 389 Processing helix chain 'K' and resid 390 through 394 Processing helix chain 'K' and resid 397 through 401 removed outlier: 3.797A pdb=" N TYR K 401 " --> pdb=" O VAL K 398 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 23 Processing helix chain 'L' and resid 50 through 69 removed outlier: 4.153A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET L 69 " --> pdb=" O PHE L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 72 No H-bonds generated for 'chain 'L' and resid 70 through 72' Processing helix chain 'L' and resid 75 through 104 removed outlier: 3.795A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 132 removed outlier: 3.575A pdb=" N MET L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL L 132 " --> pdb=" O SER L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 162 removed outlier: 3.640A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 204 through 228 Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 233 through 262 removed outlier: 3.631A pdb=" N CYS L 237 " --> pdb=" O GLY L 233 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU L 262 " --> pdb=" O SER L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 266 Processing helix chain 'L' and resid 268 through 275 Processing helix chain 'L' and resid 277 through 283 Processing helix chain 'L' and resid 292 through 321 removed outlier: 4.813A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 329 through 351 removed outlier: 3.526A pdb=" N LEU L 333 " --> pdb=" O GLY L 329 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU L 336 " --> pdb=" O ASN L 332 " (cutoff:3.500A) Proline residue: L 337 - end of helix Processing helix chain 'L' and resid 357 through 384 Processing helix chain 'L' and resid 398 through 402 removed outlier: 3.778A pdb=" N VAL L 401 " --> pdb=" O ASP L 398 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 23 Processing helix chain 'Q' and resid 47 through 69 Proline residue: Q 52 - end of helix removed outlier: 4.153A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET Q 69 " --> pdb=" O PHE Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 72 No H-bonds generated for 'chain 'Q' and resid 70 through 72' Processing helix chain 'Q' and resid 75 through 104 removed outlier: 3.795A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 132 removed outlier: 3.575A pdb=" N MET Q 115 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 162 removed outlier: 3.639A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 189 Processing helix chain 'Q' and resid 191 through 195 Processing helix chain 'Q' and resid 204 through 228 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 233 through 262 removed outlier: 3.632A pdb=" N CYS Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU Q 262 " --> pdb=" O SER Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 266 Processing helix chain 'Q' and resid 268 through 275 Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 321 removed outlier: 4.813A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 329 through 351 removed outlier: 3.527A pdb=" N LEU Q 333 " --> pdb=" O GLY Q 329 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU Q 336 " --> pdb=" O ASN Q 332 " (cutoff:3.500A) Proline residue: Q 337 - end of helix Processing helix chain 'Q' and resid 357 through 384 Processing helix chain 'Q' and resid 398 through 402 removed outlier: 3.777A pdb=" N VAL Q 401 " --> pdb=" O ASP Q 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 114 Processing helix chain 'D' and resid 88 through 114 Processing helix chain 'P' and resid 104 through 116 removed outlier: 3.879A pdb=" N LYS P 116 " --> pdb=" O ARG P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 142 Processing helix chain 'P' and resid 146 through 148 No H-bonds generated for 'chain 'P' and resid 146 through 148' Processing helix chain 'P' and resid 149 through 158 Processing helix chain 'P' and resid 163 through 167 Processing helix chain 'P' and resid 194 through 201 Processing helix chain 'P' and resid 277 through 291 Processing helix chain 'P' and resid 291 through 300 Processing helix chain 'P' and resid 303 through 317 removed outlier: 3.721A pdb=" N LEU P 307 " --> pdb=" O SER P 303 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 334 Processing helix chain 'P' and resid 335 through 347 Processing helix chain 'P' and resid 379 through 390 Processing helix chain 'P' and resid 391 through 393 No H-bonds generated for 'chain 'P' and resid 391 through 393' Processing helix chain 'P' and resid 394 through 399 Processing helix chain 'P' and resid 402 through 431 removed outlier: 3.684A pdb=" N LEU P 406 " --> pdb=" O SER P 402 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE P 414 " --> pdb=" O ILE P 410 " (cutoff:3.500A) Proline residue: P 419 - end of helix Processing helix chain 'P' and resid 436 through 455 Processing helix chain 'P' and resid 465 through 483 Processing helix chain 'P' and resid 485 through 507 Processing helix chain 'P' and resid 508 through 516 removed outlier: 3.746A pdb=" N LEU P 512 " --> pdb=" O GLY P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 517 through 547 removed outlier: 3.501A pdb=" N LEU P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 594 removed outlier: 3.557A pdb=" N ASN P 593 " --> pdb=" O ARG P 589 " (cutoff:3.500A) Processing helix chain 'P' and resid 598 through 608 Processing helix chain 'P' and resid 608 through 623 Processing helix chain 'P' and resid 660 through 667 removed outlier: 3.848A pdb=" N MET P 664 " --> pdb=" O PRO P 660 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE P 665 " --> pdb=" O ILE P 661 " (cutoff:3.500A) Processing helix chain 'P' and resid 667 through 690 Processing helix chain 'P' and resid 691 through 695 Processing helix chain 'P' and resid 701 through 719 removed outlier: 3.509A pdb=" N LEU P 718 " --> pdb=" O GLY P 714 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE P 719 " --> pdb=" O VAL P 715 " (cutoff:3.500A) Processing helix chain 'P' and resid 727 through 738 Processing helix chain 'P' and resid 760 through 772 Processing helix chain 'P' and resid 776 through 781 Processing helix chain 'P' and resid 784 through 799 removed outlier: 3.813A pdb=" N LEU P 788 " --> pdb=" O PRO P 784 " (cutoff:3.500A) Processing helix chain 'P' and resid 803 through 812 Processing helix chain 'P' and resid 813 through 814 No H-bonds generated for 'chain 'P' and resid 813 through 814' Processing helix chain 'P' and resid 815 through 819 Processing helix chain 'P' and resid 822 through 827 Processing helix chain 'P' and resid 829 through 852 Processing helix chain 'P' and resid 855 through 857 No H-bonds generated for 'chain 'P' and resid 855 through 857' Processing helix chain 'P' and resid 858 through 865 Processing helix chain 'P' and resid 865 through 878 removed outlier: 4.275A pdb=" N LEU P 874 " --> pdb=" O ARG P 870 " (cutoff:3.500A) Proline residue: P 875 - end of helix Processing helix chain 'P' and resid 879 through 887 Processing helix chain 'T' and resid 42 through 47 Processing helix chain 'T' and resid 103 through 116 removed outlier: 3.879A pdb=" N LYS T 116 " --> pdb=" O ARG T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 142 Processing helix chain 'T' and resid 146 through 148 No H-bonds generated for 'chain 'T' and resid 146 through 148' Processing helix chain 'T' and resid 149 through 158 Processing helix chain 'T' and resid 163 through 167 Processing helix chain 'T' and resid 194 through 201 Processing helix chain 'T' and resid 277 through 291 Processing helix chain 'T' and resid 291 through 300 Processing helix chain 'T' and resid 303 through 317 removed outlier: 3.721A pdb=" N LEU T 307 " --> pdb=" O SER T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 334 Processing helix chain 'T' and resid 335 through 347 Processing helix chain 'T' and resid 379 through 390 Processing helix chain 'T' and resid 391 through 393 No H-bonds generated for 'chain 'T' and resid 391 through 393' Processing helix chain 'T' and resid 394 through 399 Processing helix chain 'T' and resid 402 through 431 removed outlier: 3.682A pdb=" N LEU T 406 " --> pdb=" O SER T 402 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE T 414 " --> pdb=" O ILE T 410 " (cutoff:3.500A) Proline residue: T 419 - end of helix Processing helix chain 'T' and resid 436 through 455 Processing helix chain 'T' and resid 465 through 483 Processing helix chain 'T' and resid 485 through 507 Processing helix chain 'T' and resid 508 through 516 removed outlier: 3.747A pdb=" N LEU T 512 " --> pdb=" O GLY T 509 " (cutoff:3.500A) Processing helix chain 'T' and resid 517 through 547 removed outlier: 3.501A pdb=" N LEU T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 569 through 594 removed outlier: 3.556A pdb=" N ASN T 593 " --> pdb=" O ARG T 589 " (cutoff:3.500A) Processing helix chain 'T' and resid 598 through 608 Processing helix chain 'T' and resid 608 through 623 Processing helix chain 'T' and resid 660 through 667 removed outlier: 3.847A pdb=" N MET T 664 " --> pdb=" O PRO T 660 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE T 665 " --> pdb=" O ILE T 661 " (cutoff:3.500A) Processing helix chain 'T' and resid 667 through 690 Processing helix chain 'T' and resid 691 through 695 Processing helix chain 'T' and resid 701 through 719 removed outlier: 3.508A pdb=" N LEU T 718 " --> pdb=" O GLY T 714 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE T 719 " --> pdb=" O VAL T 715 " (cutoff:3.500A) Processing helix chain 'T' and resid 727 through 738 Processing helix chain 'T' and resid 760 through 772 Processing helix chain 'T' and resid 776 through 781 Processing helix chain 'T' and resid 784 through 799 removed outlier: 3.814A pdb=" N LEU T 788 " --> pdb=" O PRO T 784 " (cutoff:3.500A) Processing helix chain 'T' and resid 803 through 812 Processing helix chain 'T' and resid 813 through 814 No H-bonds generated for 'chain 'T' and resid 813 through 814' Processing helix chain 'T' and resid 815 through 819 Processing helix chain 'T' and resid 822 through 827 Processing helix chain 'T' and resid 829 through 852 Processing helix chain 'T' and resid 855 through 857 No H-bonds generated for 'chain 'T' and resid 855 through 857' Processing helix chain 'T' and resid 858 through 865 Processing helix chain 'T' and resid 865 through 878 removed outlier: 4.275A pdb=" N LEU T 874 " --> pdb=" O ARG T 870 " (cutoff:3.500A) Proline residue: T 875 - end of helix Processing helix chain 'T' and resid 879 through 887 Processing helix chain 'S' and resid 3 through 6 Processing helix chain 'S' and resid 7 through 33 removed outlier: 3.618A pdb=" N TRP S 11 " --> pdb=" O LYS S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 37 Processing helix chain 'S' and resid 48 through 72 removed outlier: 5.789A pdb=" N HIS S 69 " --> pdb=" O GLN S 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 86 Processing helix chain 'S' and resid 90 through 116 Processing helix chain 'S' and resid 134 through 157 Processing helix chain 'S' and resid 167 through 188 removed outlier: 5.508A pdb=" N ASP S 185 " --> pdb=" O LEU S 181 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR S 186 " --> pdb=" O LEU S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 204 removed outlier: 3.532A pdb=" N SER S 199 " --> pdb=" O ARG S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 230 Proline residue: S 216 - end of helix Processing helix chain 'S' and resid 237 through 248 removed outlier: 3.511A pdb=" N VAL S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP S 245 " --> pdb=" O ARG S 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR S 246 " --> pdb=" O VAL S 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 6 Processing helix chain 'O' and resid 7 through 33 removed outlier: 3.619A pdb=" N TRP O 11 " --> pdb=" O LYS O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 37 Processing helix chain 'O' and resid 48 through 72 removed outlier: 5.788A pdb=" N HIS O 69 " --> pdb=" O GLN O 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 86 Processing helix chain 'O' and resid 90 through 116 Processing helix chain 'O' and resid 134 through 157 Processing helix chain 'O' and resid 167 through 188 removed outlier: 5.508A pdb=" N ASP O 185 " --> pdb=" O LEU O 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR O 186 " --> pdb=" O LEU O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 204 removed outlier: 3.532A pdb=" N SER O 199 " --> pdb=" O ARG O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 230 Proline residue: O 216 - end of helix Processing helix chain 'O' and resid 237 through 248 removed outlier: 3.511A pdb=" N VAL O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP O 245 " --> pdb=" O ARG O 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 6 Processing helix chain 'R' and resid 7 through 33 removed outlier: 3.618A pdb=" N TRP R 11 " --> pdb=" O LYS R 7 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 37 Processing helix chain 'R' and resid 48 through 72 removed outlier: 5.788A pdb=" N HIS R 69 " --> pdb=" O GLN R 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 90 through 116 Processing helix chain 'R' and resid 134 through 157 Processing helix chain 'R' and resid 167 through 188 removed outlier: 5.508A pdb=" N ASP R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.532A pdb=" N SER R 199 " --> pdb=" O ARG R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 230 Proline residue: R 216 - end of helix Processing helix chain 'R' and resid 237 through 248 removed outlier: 3.511A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 6 Processing helix chain 'M' and resid 7 through 33 removed outlier: 3.619A pdb=" N TRP M 11 " --> pdb=" O LYS M 7 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 37 Processing helix chain 'M' and resid 48 through 72 removed outlier: 5.788A pdb=" N HIS M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE M 70 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 86 Processing helix chain 'M' and resid 90 through 116 Processing helix chain 'M' and resid 134 through 157 Processing helix chain 'M' and resid 167 through 188 removed outlier: 5.508A pdb=" N ASP M 185 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR M 186 " --> pdb=" O LEU M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 204 removed outlier: 3.533A pdb=" N SER M 199 " --> pdb=" O ARG M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 230 Proline residue: M 216 - end of helix Processing helix chain 'M' and resid 237 through 248 removed outlier: 3.511A pdb=" N VAL M 244 " --> pdb=" O ASP M 240 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP M 245 " --> pdb=" O ARG M 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR M 246 " --> pdb=" O VAL M 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.590A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.584A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.309A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.309A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL X 288 " --> pdb=" O LYS X 421 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS X 421 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE X 292 " --> pdb=" O ASN X 417 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN X 417 " --> pdb=" O PHE X 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 303 through 308 removed outlier: 5.968A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.294A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 408 through 409 removed outlier: 6.294A pdb=" N ASP X 408 " --> pdb=" O PHE X 578 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLN X 580 " --> pdb=" O ASP X 408 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA X 515 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS X 525 " --> pdb=" O ALA X 515 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AB1, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB2, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.656A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY X 627 " --> pdb=" O ARG X 633 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG X 633 " --> pdb=" O GLY X 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 32 through 34 Processing sheet with id=AB4, first strand: chain 'L' and resid 24 through 25 Processing sheet with id=AB5, first strand: chain 'Q' and resid 24 through 25 Processing sheet with id=AB6, first strand: chain 'P' and resid 85 through 87 removed outlier: 6.327A pdb=" N LEU P 73 " --> pdb=" O ASP P 67 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP P 67 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP P 75 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL P 65 " --> pdb=" O TRP P 75 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU P 77 " --> pdb=" O GLU P 63 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU P 63 " --> pdb=" O GLU P 77 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 118 through 123 removed outlier: 4.188A pdb=" N VAL P 119 " --> pdb=" O PHE P 244 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG P 246 " --> pdb=" O VAL P 119 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU P 121 " --> pdb=" O ARG P 246 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN P 248 " --> pdb=" O LEU P 121 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU P 123 " --> pdb=" O GLN P 248 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA P 250 " --> pdb=" O LEU P 123 " (cutoff:3.500A) removed outlier: 12.084A pdb=" N GLY P 243 " --> pdb=" O GLY P 270 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N GLY P 270 " --> pdb=" O GLY P 243 " (cutoff:3.500A) removed outlier: 12.502A pdb=" N VAL P 245 " --> pdb=" O LEU P 268 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N LEU P 268 " --> pdb=" O VAL P 245 " (cutoff:3.500A) removed outlier: 12.038A pdb=" N LEU P 247 " --> pdb=" O PHE P 266 " (cutoff:3.500A) removed outlier: 12.023A pdb=" N PHE P 266 " --> pdb=" O LEU P 247 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N GLU P 249 " --> pdb=" O PHE P 264 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE P 264 " --> pdb=" O GLU P 249 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA P 226 " --> pdb=" O ILE P 262 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE P 264 " --> pdb=" O ALA P 226 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY P 270 " --> pdb=" O GLY P 232 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG P 233 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N MET P 66 " --> pdb=" O ARG P 233 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU P 63 " --> pdb=" O GLU P 77 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLU P 77 " --> pdb=" O GLU P 63 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL P 65 " --> pdb=" O TRP P 75 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N TRP P 75 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP P 67 " --> pdb=" O LEU P 73 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU P 73 " --> pdb=" O ASP P 67 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'P' and resid 102 through 103 Processing sheet with id=AB9, first strand: chain 'P' and resid 462 through 463 Processing sheet with id=AC1, first strand: chain 'P' and resid 739 through 742 removed outlier: 6.901A pdb=" N VAL P 740 " --> pdb=" O GLN P 754 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN P 752 " --> pdb=" O GLY P 742 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 85 through 87 removed outlier: 6.326A pdb=" N LEU T 73 " --> pdb=" O ASP T 67 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP T 67 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP T 75 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL T 65 " --> pdb=" O TRP T 75 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU T 77 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU T 63 " --> pdb=" O GLU T 77 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 118 through 123 removed outlier: 4.187A pdb=" N VAL T 119 " --> pdb=" O PHE T 244 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ARG T 246 " --> pdb=" O VAL T 119 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU T 121 " --> pdb=" O ARG T 246 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLN T 248 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU T 123 " --> pdb=" O GLN T 248 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA T 250 " --> pdb=" O LEU T 123 " (cutoff:3.500A) removed outlier: 12.085A pdb=" N GLY T 243 " --> pdb=" O GLY T 270 " (cutoff:3.500A) removed outlier: 11.464A pdb=" N GLY T 270 " --> pdb=" O GLY T 243 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N VAL T 245 " --> pdb=" O LEU T 268 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N LEU T 268 " --> pdb=" O VAL T 245 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N LEU T 247 " --> pdb=" O PHE T 266 " (cutoff:3.500A) removed outlier: 12.022A pdb=" N PHE T 266 " --> pdb=" O LEU T 247 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N GLU T 249 " --> pdb=" O PHE T 264 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE T 264 " --> pdb=" O GLU T 249 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ALA T 226 " --> pdb=" O ILE T 262 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE T 264 " --> pdb=" O ALA T 226 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY T 270 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG T 233 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 9.905A pdb=" N MET T 66 " --> pdb=" O ARG T 233 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU T 63 " --> pdb=" O GLU T 77 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU T 77 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL T 65 " --> pdb=" O TRP T 75 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP T 75 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASP T 67 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU T 73 " --> pdb=" O ASP T 67 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 462 through 463 Processing sheet with id=AC5, first strand: chain 'T' and resid 739 through 742 removed outlier: 6.901A pdb=" N VAL T 740 " --> pdb=" O GLN T 754 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN T 752 " --> pdb=" O GLY T 742 " (cutoff:3.500A) 2389 hydrogen bonds defined for protein. 6958 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: 9.87 Time building geometry restraints manager: 3.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6074 1.31 - 1.43: 10428 1.43 - 1.56: 22922 1.56 - 1.69: 8 1.69 - 1.81: 291 Bond restraints: 39723 Sorted by residual: bond pdb=" C1B PIO T1004 " pdb=" O3C PIO T1004 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" C1B PIO P1004 " pdb=" O3C PIO P1004 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1A PIO P1004 " pdb=" O2C PIO P1004 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C1A PIO T1004 " pdb=" O2C PIO T1004 " ideal model delta sigma weight residual 1.332 1.398 -0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 39718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 53497 2.40 - 4.81: 478 4.81 - 7.21: 73 7.21 - 9.61: 7 9.61 - 12.02: 4 Bond angle restraints: 54059 Sorted by residual: angle pdb=" N LEU Q 189 " pdb=" CA LEU Q 189 " pdb=" C LEU Q 189 " ideal model delta sigma weight residual 113.02 107.15 5.87 1.20e+00 6.94e-01 2.40e+01 angle pdb=" C TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta sigma weight residual 110.79 118.53 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" N ASP X 408 " pdb=" CA ASP X 408 " pdb=" C ASP X 408 " ideal model delta sigma weight residual 109.96 103.41 6.55 1.50e+00 4.44e-01 1.91e+01 angle pdb=" CA VAL Q 374 " pdb=" C VAL Q 374 " pdb=" O VAL Q 374 " ideal model delta sigma weight residual 120.85 116.30 4.55 1.06e+00 8.90e-01 1.84e+01 angle pdb=" O1 PIO T1004 " pdb=" P1 PIO T1004 " pdb=" O13 PIO T1004 " ideal model delta sigma weight residual 97.64 109.66 -12.02 3.00e+00 1.11e-01 1.60e+01 ... (remaining 54054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 22517 23.90 - 47.81: 575 47.81 - 71.71: 115 71.71 - 95.61: 24 95.61 - 119.52: 1 Dihedral angle restraints: 23232 sinusoidal: 8971 harmonic: 14261 Sorted by residual: dihedral pdb=" C TYR Q 180 " pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta harmonic sigma weight residual -122.60 -134.40 11.80 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" CA LEU O 182 " pdb=" C LEU O 182 " pdb=" N ALA O 183 " pdb=" CA ALA O 183 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU S 182 " pdb=" C LEU S 182 " pdb=" N ALA S 183 " pdb=" CA ALA S 183 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 23229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5822 0.066 - 0.132: 556 0.132 - 0.199: 24 0.199 - 0.265: 2 0.265 - 0.331: 4 Chirality restraints: 6408 Sorted by residual: chirality pdb=" CA TYR Q 180 " pdb=" N TYR Q 180 " pdb=" C TYR Q 180 " pdb=" CB TYR Q 180 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C11 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" C12 AJP Q 502 " pdb=" C16 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 6405 not shown) Planarity restraints: 6700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 576 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C SER X 576 " -0.053 2.00e-02 2.50e+03 pdb=" O SER X 576 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS X 577 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 403 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C THR X 403 " 0.045 2.00e-02 2.50e+03 pdb=" O THR X 403 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU X 404 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 407 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR X 407 " -0.040 2.00e-02 2.50e+03 pdb=" O THR X 407 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP X 408 " 0.014 2.00e-02 2.50e+03 ... (remaining 6697 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4161 2.75 - 3.29: 38734 3.29 - 3.83: 69728 3.83 - 4.36: 80497 4.36 - 4.90: 139455 Nonbonded interactions: 332575 Sorted by model distance: nonbonded pdb=" O PHE K 28 " pdb=" OG1 THR K 32 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.239 3.040 nonbonded pdb=" OG SER X 91 " pdb=" OG1 THR X 107 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU X 634 " pdb=" OG1 THR T 42 " model vdw 2.275 3.040 nonbonded pdb=" O ARG X 194 " pdb=" OG SER X 197 " model vdw 2.289 3.040 ... (remaining 332570 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: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'N' } ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } ncs_group { reference = (chain 'M' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'O' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'R' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'S' and (resid 3 through 233 or resid 235 through 249)) } ncs_group { reference = (chain 'P' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348 or resid 371 through 1004)) selection = (chain 'T' and (resid 56 through 203 or resid 217 through 1004)) } 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=0.45 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: 8.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 36.820 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.120 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:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.003 0.069 39725 Z= 0.166 Angle : 0.565 12.018 54065 Z= 0.318 Chirality : 0.040 0.331 6408 Planarity : 0.004 0.055 6698 Dihedral : 11.303 119.518 14052 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % Rotamer: Outliers : 2.34 % Allowed : 4.43 % Favored : 93.23 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.12), residues: 4925 helix: 2.01 (0.09), residues: 2841 sheet: 1.44 (0.29), residues: 345 loop : 0.28 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG T 246 TYR 0.025 0.001 TYR Q 180 PHE 0.018 0.001 PHE Q 181 TRP 0.010 0.001 TRP X 90 HIS 0.006 0.001 HIS Q 325 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.17 (39723) covalent geometry : angle 0.56517 / 0.32 (54059) hydrogen bonds : bond 0.13239 / 9.07 ( 2377) hydrogen bonds : angle 5.40260 / 3.81 ( 6958) link_NAG-ASN : bond 0.00100 / 0.05 ( 2) link_NAG-ASN : angle 0.99004 / 0.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 846 time to evaluate : 1.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LYS cc_start: 0.7658 (tptm) cc_final: 0.7329 (tmtt) REVERT: A 270 LYS cc_start: 0.7632 (pttm) cc_final: 0.7261 (ptpt) REVERT: A 281 ARG cc_start: 0.8466 (ptm160) cc_final: 0.8251 (ttp-170) REVERT: A 337 ASP cc_start: 0.7582 (m-30) cc_final: 0.7342 (m-30) REVERT: A 455 TYR cc_start: 0.7611 (t80) cc_final: 0.7410 (t80) REVERT: X 224 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7370 (mm-30) REVERT: X 311 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6920 (tp30) REVERT: X 406 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (tp) REVERT: X 483 SER cc_start: 0.8011 (p) cc_final: 0.7736 (m) REVERT: X 507 VAL cc_start: 0.8390 (p) cc_final: 0.8166 (t) REVERT: K 11 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6834 (mtt90) REVERT: K 33 HIS cc_start: 0.6387 (t-90) cc_final: 0.6134 (t-170) REVERT: K 178 TYR cc_start: 0.7789 (m-80) cc_final: 0.7577 (m-80) REVERT: K 328 MET cc_start: 0.5110 (ptm) cc_final: 0.4895 (ptm) REVERT: K 335 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6563 (mt) REVERT: K 340 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6605 (mm-30) REVERT: K 364 LEU cc_start: 0.6031 (OUTLIER) cc_final: 0.5597 (pp) REVERT: K 374 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7679 (mp) REVERT: L 157 TYR cc_start: 0.7568 (t80) cc_final: 0.7249 (t80) REVERT: L 387 LEU cc_start: 0.7699 (mt) cc_final: 0.7448 (mm) REVERT: Q 208 ASP cc_start: 0.7465 (m-30) cc_final: 0.7210 (m-30) REVERT: D 100 MET cc_start: 0.2976 (ttm) cc_final: 0.1928 (tmm) REVERT: P 167 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7176 (tp) REVERT: P 179 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6473 (p) REVERT: P 289 MET cc_start: 0.7791 (tpt) cc_final: 0.6540 (tpt) REVERT: P 646 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7204 (ptm160) REVERT: T 32 GLU cc_start: 0.6377 (tt0) cc_final: 0.6028 (tt0) REVERT: T 289 MET cc_start: 0.8979 (tpt) cc_final: 0.8610 (mmm) REVERT: T 770 VAL cc_start: 0.7641 (t) cc_final: 0.7373 (t) outliers start: 95 outliers final: 16 residues processed: 908 average time/residue: 0.6843 time to fit residues: 761.4543 Evaluate side-chains 657 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 632 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 340 GLU Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain K residue 374 ILE Chi-restraints excluded: chain Q residue 302 ILE Chi-restraints excluded: chain Q residue 349 VAL Chi-restraints excluded: chain Q residue 377 LEU Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 486 TYR Chi-restraints excluded: chain T residue 560 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 137 GLN A 165 ASN A 183 ASN A 215 HIS A 237 GLN A 251 ASN A 350 HIS W 18 GLN X 133 GLN X 151 ASN X 154 GLN X 433 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 632 HIS X 646 ASN K 41 GLN K 49 GLN K 52 GLN K 236 ASN K 260 HIS L 98 GLN L 117 ASN L 292 HIS L 395 ASN Q 55 GLN Q 98 GLN Q 102 GLN P 198 GLN P 330 GLN P 377 GLN P 457 GLN P 630 GLN P 651 HIS P 683 GLN P 819 HIS T 37 HIS T 330 GLN T 377 GLN T 457 GLN T 545 GLN T 630 GLN T 651 HIS T 683 GLN T 819 HIS S 122 ASN R 101 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.102221 restraints weight = 130074.129| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.66 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39725 Z= 0.158 Angle : 0.541 8.850 54065 Z= 0.280 Chirality : 0.040 0.167 6408 Planarity : 0.005 0.051 6698 Dihedral : 6.181 108.077 5545 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.45 % Favored : 98.43 % Rotamer: Outliers : 2.56 % Allowed : 10.94 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.12), residues: 4925 helix: 2.16 (0.10), residues: 2875 sheet: 1.35 (0.29), residues: 332 loop : 0.36 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 95 TYR 0.018 0.002 TYR Q 206 PHE 0.022 0.002 PHE Q 62 TRP 0.013 0.001 TRP T 492 HIS 0.007 0.001 HIS L 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 (39723) covalent geometry : angle 0.54124 / 0.28 (54059) hydrogen bonds : bond 0.04722 / 3.26 ( 2377) hydrogen bonds : angle 4.64262 / 3.27 ( 6958) link_NAG-ASN : bond 0.00256 / 0.13 ( 2) link_NAG-ASN : angle 0.63501 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 671 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 337 ASP cc_start: 0.7217 (m-30) cc_final: 0.7006 (m-30) REVERT: X 96 GLU cc_start: 0.7218 (tp30) cc_final: 0.6980 (mm-30) REVERT: X 311 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6815 (tp30) REVERT: X 406 LEU cc_start: 0.8570 (tt) cc_final: 0.8165 (tp) REVERT: X 408 ASP cc_start: 0.7445 (t0) cc_final: 0.7129 (t70) REVERT: X 646 ASN cc_start: 0.7601 (m110) cc_final: 0.7326 (m-40) REVERT: K 11 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6623 (mtt90) REVERT: K 178 TYR cc_start: 0.7658 (m-80) cc_final: 0.7426 (m-80) REVERT: K 364 LEU cc_start: 0.6307 (OUTLIER) cc_final: 0.6020 (pp) REVERT: L 157 TYR cc_start: 0.7677 (t80) cc_final: 0.7376 (t80) REVERT: L 369 ILE cc_start: 0.7659 (mt) cc_final: 0.7440 (mm) REVERT: Q 208 ASP cc_start: 0.7458 (m-30) cc_final: 0.7169 (m-30) REVERT: Q 321 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7725 (mptt) REVERT: D 100 MET cc_start: 0.3449 (ttm) cc_final: 0.2041 (tmm) REVERT: P 60 GLU cc_start: 0.7728 (tt0) cc_final: 0.7524 (tt0) REVERT: P 77 GLU cc_start: 0.7825 (pt0) cc_final: 0.7509 (pt0) REVERT: P 167 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6989 (tp) REVERT: P 179 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6379 (p) REVERT: P 289 MET cc_start: 0.7696 (tpt) cc_final: 0.7062 (tpt) REVERT: P 306 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: P 590 LYS cc_start: 0.7300 (pptt) cc_final: 0.6938 (pttp) REVERT: T 417 LEU cc_start: 0.8042 (tp) cc_final: 0.7573 (tp) REVERT: T 559 MET cc_start: 0.5585 (mmm) cc_final: 0.5264 (mmm) REVERT: S 191 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7299 (mm) REVERT: O 49 ASN cc_start: 0.8038 (m-40) cc_final: 0.7757 (m-40) outliers start: 103 outliers final: 35 residues processed: 715 average time/residue: 0.6814 time to fit residues: 596.5904 Evaluate side-chains 664 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 622 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 492 GLN Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain X residue 647 THR Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 68 ASN Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 174 VAL Chi-restraints excluded: chain K residue 200 GLN Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 292 HIS Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 306 GLU Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 650 ILE Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 341 GLU Chi-restraints excluded: chain T residue 486 TYR Chi-restraints excluded: chain T residue 595 SER Chi-restraints excluded: chain T residue 601 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain M residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 345 optimal weight: 0.8980 chunk 373 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 469 optimal weight: 0.8980 chunk 268 optimal weight: 0.9990 chunk 247 optimal weight: 0.7980 chunk 424 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 171 optimal weight: 0.5980 chunk 152 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 133 ASN A 165 ASN W 18 GLN X 151 ASN X 570 HIS K 49 GLN L 98 GLN L 117 ASN L 292 HIS Q 55 GLN Q 98 GLN T 545 GLN T 554 ASN T 736 ASN S 122 ASN M 88 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.121965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100846 restraints weight = 114065.136| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.26 r_work: 0.2830 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39725 Z= 0.136 Angle : 0.521 8.179 54065 Z= 0.268 Chirality : 0.040 0.202 6408 Planarity : 0.004 0.049 6698 Dihedral : 6.012 107.434 5526 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.67 % Favored : 98.21 % Rotamer: Outliers : 2.61 % Allowed : 12.09 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.12), residues: 4925 helix: 2.16 (0.10), residues: 2887 sheet: 1.01 (0.28), residues: 340 loop : 0.32 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 154 TYR 0.022 0.002 TYR A 455 PHE 0.026 0.002 PHE P 476 TRP 0.012 0.001 TRP T 492 HIS 0.009 0.001 HIS X 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (39723) covalent geometry : angle 0.52133 / 0.27 (54059) hydrogen bonds : bond 0.04411 / 3.05 ( 2377) hydrogen bonds : angle 4.54699 / 3.20 ( 6958) link_NAG-ASN : bond 0.00209 / 0.11 ( 2) link_NAG-ASN : angle 0.75341 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 635 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7336 (ttp-170) REVERT: A 117 MET cc_start: 0.8611 (mtt) cc_final: 0.8034 (mtt) REVERT: A 451 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: X 96 GLU cc_start: 0.7976 (tp30) cc_final: 0.7692 (mm-30) REVERT: X 310 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: X 311 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7086 (tp30) REVERT: X 406 LEU cc_start: 0.8700 (tt) cc_final: 0.8373 (tp) REVERT: X 408 ASP cc_start: 0.7876 (t0) cc_final: 0.7655 (t70) REVERT: X 599 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7289 (tm-30) REVERT: X 646 ASN cc_start: 0.7743 (m110) cc_final: 0.7467 (m-40) REVERT: X 672 MET cc_start: 0.8174 (mmp) cc_final: 0.7675 (mmm) REVERT: K 11 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7087 (mtt90) REVERT: K 16 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6208 (t-100) REVERT: K 44 LEU cc_start: 0.7899 (tp) cc_final: 0.7674 (tt) REVERT: K 178 TYR cc_start: 0.8297 (m-80) cc_final: 0.7742 (m-80) REVERT: K 204 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7053 (mt) REVERT: K 364 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5478 (pp) REVERT: L 157 TYR cc_start: 0.8035 (t80) cc_final: 0.7819 (t80) REVERT: Q 100 ILE cc_start: 0.8650 (mm) cc_final: 0.8411 (tp) REVERT: Q 208 ASP cc_start: 0.7953 (m-30) cc_final: 0.7689 (m-30) REVERT: Q 231 GLU cc_start: 0.7204 (tp30) cc_final: 0.6991 (tp30) REVERT: Q 321 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7944 (mptt) REVERT: D 100 MET cc_start: 0.3501 (ttm) cc_final: 0.1647 (tmm) REVERT: P 77 GLU cc_start: 0.8445 (pt0) cc_final: 0.8165 (pt0) REVERT: P 167 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7263 (tp) REVERT: P 179 THR cc_start: 0.7347 (OUTLIER) cc_final: 0.7031 (p) REVERT: P 289 MET cc_start: 0.8258 (tpt) cc_final: 0.7672 (tpt) REVERT: P 740 VAL cc_start: 0.7400 (t) cc_final: 0.6898 (m) REVERT: P 798 THR cc_start: 0.8174 (m) cc_final: 0.7723 (p) REVERT: T 124 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8026 (mm-40) REVERT: T 324 THR cc_start: 0.4897 (OUTLIER) cc_final: 0.4468 (p) REVERT: T 417 LEU cc_start: 0.8067 (tp) cc_final: 0.7797 (tp) REVERT: T 559 MET cc_start: 0.6047 (mmm) cc_final: 0.5635 (mmm) REVERT: T 605 ILE cc_start: 0.8498 (mm) cc_final: 0.8193 (mt) REVERT: T 608 PHE cc_start: 0.7966 (m-10) cc_final: 0.7752 (m-80) REVERT: T 839 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7103 (mt) REVERT: S 191 ILE cc_start: 0.7804 (OUTLIER) cc_final: 0.7485 (mm) REVERT: O 5 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7518 (t80) REVERT: O 49 ASN cc_start: 0.8265 (m-40) cc_final: 0.8054 (m-40) REVERT: O 157 THR cc_start: 0.8580 (p) cc_final: 0.8332 (p) REVERT: M 88 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8272 (mm110) outliers start: 105 outliers final: 37 residues processed: 684 average time/residue: 0.6961 time to fit residues: 581.0173 Evaluate side-chains 653 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 601 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain X residue 127 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 364 LEU Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 292 HIS Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain P residue 727 THR Chi-restraints excluded: chain P residue 881 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 324 THR Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 341 GLU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 486 TYR Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 601 LEU Chi-restraints excluded: chain T residue 657 SER Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 839 ILE Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 5 PHE Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain M residue 238 LEU Chi-restraints excluded: chain M residue 246 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 36 optimal weight: 0.8980 chunk 203 optimal weight: 0.0870 chunk 255 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 353 optimal weight: 4.9990 chunk 349 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 392 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 165 ASN X 133 GLN X 151 ASN X 154 GLN X 517 HIS L 117 ASN L 292 HIS T 545 GLN S 122 ASN ** M 74 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 = 0.3568 r_free = 0.3568 target = 0.121619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.100446 restraints weight = 119166.517| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.38 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39725 Z= 0.130 Angle : 0.513 8.302 54065 Z= 0.263 Chirality : 0.039 0.213 6408 Planarity : 0.004 0.047 6698 Dihedral : 5.937 106.844 5523 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.55 % Favored : 98.35 % Rotamer: Outliers : 2.46 % Allowed : 12.76 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.12), residues: 4925 helix: 2.19 (0.10), residues: 2889 sheet: 0.90 (0.27), residues: 345 loop : 0.28 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 154 TYR 0.025 0.002 TYR A 455 PHE 0.029 0.002 PHE T 789 TRP 0.012 0.001 TRP K 16 HIS 0.007 0.001 HIS X 570 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (39723) covalent geometry : angle 0.51271 / 0.26 (54059) hydrogen bonds : bond 0.04272 / 2.95 ( 2377) hydrogen bonds : angle 4.52231 / 3.18 ( 6958) link_NAG-ASN : bond 0.00195 / 0.10 ( 2) link_NAG-ASN : angle 0.77177 / 0.44 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 601 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7040 (ttp-170) REVERT: A 96 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6927 (tp30) REVERT: A 451 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: X 87 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7119 (mmp-170) REVERT: X 96 GLU cc_start: 0.7080 (tp30) cc_final: 0.6826 (mm-30) REVERT: X 133 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7153 (mm110) REVERT: X 310 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: X 406 LEU cc_start: 0.8500 (tt) cc_final: 0.8257 (tp) REVERT: X 408 ASP cc_start: 0.7465 (t0) cc_final: 0.7203 (t70) REVERT: X 646 ASN cc_start: 0.7514 (m110) cc_final: 0.7258 (m-40) REVERT: K 11 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6600 (mtt90) REVERT: K 44 LEU cc_start: 0.7969 (tp) cc_final: 0.7728 (tt) REVERT: K 204 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6995 (mt) REVERT: L 98 GLN cc_start: 0.7950 (mt0) cc_final: 0.7743 (mt0) REVERT: L 157 TYR cc_start: 0.7793 (t80) cc_final: 0.7553 (t80) REVERT: Q 100 ILE cc_start: 0.8580 (mm) cc_final: 0.8363 (tp) REVERT: Q 208 ASP cc_start: 0.7533 (m-30) cc_final: 0.7235 (m-30) REVERT: Q 321 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7718 (mptt) REVERT: D 100 MET cc_start: 0.3537 (ttm) cc_final: 0.1974 (tmm) REVERT: P 167 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7084 (tp) REVERT: P 179 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6377 (p) REVERT: P 289 MET cc_start: 0.7705 (tpt) cc_final: 0.7073 (tpt) REVERT: P 740 VAL cc_start: 0.7361 (t) cc_final: 0.7089 (m) REVERT: T 124 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6996 (mm-40) REVERT: T 417 LEU cc_start: 0.7943 (tp) cc_final: 0.7613 (tp) REVERT: T 559 MET cc_start: 0.5519 (mmm) cc_final: 0.5153 (mmm) REVERT: T 605 ILE cc_start: 0.8426 (mm) cc_final: 0.8186 (mt) REVERT: S 81 LEU cc_start: 0.8360 (tm) cc_final: 0.8064 (tp) REVERT: S 191 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7252 (mm) REVERT: O 49 ASN cc_start: 0.7976 (m-40) cc_final: 0.7755 (m-40) REVERT: O 157 THR cc_start: 0.8523 (p) cc_final: 0.8281 (p) REVERT: M 88 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7668 (mm-40) outliers start: 99 outliers final: 37 residues processed: 650 average time/residue: 0.7200 time to fit residues: 571.2605 Evaluate side-chains 645 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 596 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 239 GLN Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain P residue 877 ILE Chi-restraints excluded: chain P residue 881 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 601 LEU Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 657 SER Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 846 VAL Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain R residue 91 ILE Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain M residue 246 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 356 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 400 optimal weight: 0.5980 chunk 372 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 363 optimal weight: 0.7980 chunk 458 optimal weight: 4.9990 chunk 456 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN W 18 GLN X 151 ASN X 154 GLN ** X 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 117 ASN L 292 HIS L 395 ASN T 545 GLN S 122 ASN M 74 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.100089 restraints weight = 121890.663| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.43 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39725 Z= 0.124 Angle : 0.509 8.687 54065 Z= 0.260 Chirality : 0.039 0.218 6408 Planarity : 0.004 0.047 6698 Dihedral : 5.857 106.614 5519 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.71 % Favored : 98.19 % Rotamer: Outliers : 2.41 % Allowed : 13.25 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.12), residues: 4925 helix: 2.21 (0.10), residues: 2889 sheet: 0.82 (0.28), residues: 340 loop : 0.29 (0.15), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 295 TYR 0.023 0.002 TYR A 455 PHE 0.032 0.001 PHE T 789 TRP 0.011 0.001 TRP K 16 HIS 0.006 0.001 HIS T 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (39723) covalent geometry : angle 0.50937 / 0.26 (54059) hydrogen bonds : bond 0.04189 / 2.90 ( 2377) hydrogen bonds : angle 4.51087 / 3.17 ( 6958) link_NAG-ASN : bond 0.00191 / 0.10 ( 2) link_NAG-ASN : angle 0.80731 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 603 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7049 (ttp-170) REVERT: A 451 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: X 87 ARG cc_start: 0.7400 (mtp180) cc_final: 0.7126 (mmp-170) REVERT: X 310 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: X 406 LEU cc_start: 0.8493 (tt) cc_final: 0.8241 (tp) REVERT: X 408 ASP cc_start: 0.7420 (t0) cc_final: 0.7199 (t70) REVERT: X 488 ARG cc_start: 0.7490 (mmm160) cc_final: 0.7097 (mmm160) REVERT: X 587 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.6956 (mtp85) REVERT: X 646 ASN cc_start: 0.7521 (m110) cc_final: 0.7250 (m-40) REVERT: X 672 MET cc_start: 0.7844 (mmp) cc_final: 0.7353 (mmm) REVERT: K 11 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.6562 (mtt90) REVERT: K 44 LEU cc_start: 0.7947 (tp) cc_final: 0.7719 (tt) REVERT: K 204 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6972 (mt) REVERT: L 98 GLN cc_start: 0.7962 (mt0) cc_final: 0.7746 (mt0) REVERT: L 157 TYR cc_start: 0.7810 (t80) cc_final: 0.7585 (t80) REVERT: Q 100 ILE cc_start: 0.8581 (mm) cc_final: 0.8381 (tp) REVERT: Q 208 ASP cc_start: 0.7555 (m-30) cc_final: 0.7265 (m-30) REVERT: Q 321 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7708 (mptt) REVERT: D 100 MET cc_start: 0.3579 (ttm) cc_final: 0.2010 (tmm) REVERT: P 167 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7010 (tp) REVERT: P 179 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6360 (p) REVERT: P 289 MET cc_start: 0.7709 (tpt) cc_final: 0.7119 (tpt) REVERT: P 615 LEU cc_start: 0.7006 (tt) cc_final: 0.6787 (tp) REVERT: P 833 MET cc_start: 0.7549 (ttp) cc_final: 0.7289 (ttp) REVERT: T 124 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6977 (mm-40) REVERT: T 306 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7726 (mt-10) REVERT: T 417 LEU cc_start: 0.7966 (tp) cc_final: 0.7617 (tp) REVERT: T 559 MET cc_start: 0.5470 (mmm) cc_final: 0.5133 (mmm) REVERT: S 81 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8041 (tp) REVERT: S 191 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7238 (mm) REVERT: O 157 THR cc_start: 0.8483 (p) cc_final: 0.8203 (p) outliers start: 97 outliers final: 45 residues processed: 651 average time/residue: 0.7096 time to fit residues: 562.3925 Evaluate side-chains 645 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 587 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 321 LYS Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 191 GLN Chi-restraints excluded: chain P residue 239 GLN Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain P residue 881 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 306 GLU Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 343 LEU Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 657 SER Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 846 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain R residue 96 MET Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain M residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 344 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 291 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 413 optimal weight: 2.9990 chunk 351 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 483 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN W 18 GLN X 122 GLN X 133 GLN X 151 ASN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN ** X 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 674 GLN L 117 ASN L 292 HIS D 82 GLN T 545 GLN S 122 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097608 restraints weight = 121957.345| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.44 r_work: 0.2774 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2764 r_free = 0.2764 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2764 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 39725 Z= 0.203 Angle : 0.601 8.822 54065 Z= 0.309 Chirality : 0.043 0.243 6408 Planarity : 0.005 0.050 6698 Dihedral : 6.209 107.220 5519 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 2.68 % Allowed : 13.40 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.12), residues: 4925 helix: 1.94 (0.10), residues: 2867 sheet: 0.59 (0.27), residues: 351 loop : 0.16 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 155 TYR 0.028 0.002 TYR A 455 PHE 0.034 0.002 PHE T 789 TRP 0.021 0.002 TRP K 220 HIS 0.007 0.002 HIS M 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (39723) covalent geometry : angle 0.60110 / 0.31 (54059) hydrogen bonds : bond 0.05106 / 3.53 ( 2377) hydrogen bonds : angle 4.74389 / 3.34 ( 6958) link_NAG-ASN : bond 0.00120 / 0.06 ( 2) link_NAG-ASN : angle 0.82498 / 0.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 628 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: A 451 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: X 87 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7394 (mmp-170) REVERT: X 310 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: X 406 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8398 (tp) REVERT: X 492 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7774 (mp10) REVERT: X 548 PHE cc_start: 0.8083 (m-80) cc_final: 0.7683 (m-80) REVERT: X 587 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7056 (mtp85) REVERT: X 599 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7530 (tm-30) REVERT: K 11 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7019 (mtt90) REVERT: K 16 TRP cc_start: 0.7121 (OUTLIER) cc_final: 0.6208 (t-100) REVERT: K 44 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7718 (tt) REVERT: K 204 ILE cc_start: 0.7499 (OUTLIER) cc_final: 0.7236 (mt) REVERT: L 164 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7836 (mttp) REVERT: L 407 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7948 (mppt) REVERT: Q 262 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7443 (mm-30) REVERT: P 77 GLU cc_start: 0.8489 (pt0) cc_final: 0.8118 (pt0) REVERT: P 83 GLN cc_start: 0.8032 (tp40) cc_final: 0.7638 (tt0) REVERT: P 163 HIS cc_start: 0.7579 (m-70) cc_final: 0.7367 (m90) REVERT: P 167 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7436 (tp) REVERT: P 179 THR cc_start: 0.7351 (OUTLIER) cc_final: 0.6979 (p) REVERT: P 289 MET cc_start: 0.8212 (tpt) cc_final: 0.7752 (tpt) REVERT: P 628 TYR cc_start: 0.8374 (t80) cc_final: 0.8147 (t80) REVERT: P 740 VAL cc_start: 0.7171 (t) cc_final: 0.6603 (m) REVERT: P 833 MET cc_start: 0.8118 (ttp) cc_final: 0.7880 (ttp) REVERT: T 124 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: T 174 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7925 (mmtm) REVERT: T 198 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: T 306 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: T 559 MET cc_start: 0.5955 (mmm) cc_final: 0.5525 (mmm) REVERT: S 191 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7470 (mm) outliers start: 108 outliers final: 49 residues processed: 683 average time/residue: 0.7260 time to fit residues: 604.2576 Evaluate side-chains 671 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 605 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 492 GLN Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 314 LEU Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 191 GLN Chi-restraints excluded: chain P residue 239 GLN Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain P residue 881 VAL Chi-restraints excluded: chain T residue 69 LYS Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 198 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 306 GLU Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 528 ILE Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 696 MET Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain T residue 846 VAL Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 37 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 444 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 477 optimal weight: 2.9990 chunk 387 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 258 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 217 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN X 133 GLN X 151 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN X 646 ASN L 117 ASN L 292 HIS P 133 ASN P 339 GLN T 545 GLN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098409 restraints weight = 136567.529| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 3.78 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39725 Z= 0.132 Angle : 0.534 9.949 54065 Z= 0.273 Chirality : 0.039 0.249 6408 Planarity : 0.004 0.047 6698 Dihedral : 6.015 105.993 5519 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.87 % Favored : 98.02 % Rotamer: Outliers : 2.27 % Allowed : 14.24 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.12), residues: 4925 helix: 2.07 (0.10), residues: 2874 sheet: 0.59 (0.27), residues: 346 loop : 0.19 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 155 TYR 0.024 0.002 TYR A 455 PHE 0.037 0.002 PHE T 789 TRP 0.012 0.001 TRP P 81 HIS 0.006 0.001 HIS T 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (39723) covalent geometry : angle 0.53415 / 0.27 (54059) hydrogen bonds : bond 0.04377 / 3.02 ( 2377) hydrogen bonds : angle 4.60580 / 3.24 ( 6958) link_NAG-ASN : bond 0.00198 / 0.10 ( 2) link_NAG-ASN : angle 0.86119 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 613 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7069 (ttp-170) REVERT: A 92 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7190 (mp0) REVERT: A 451 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6531 (mp0) REVERT: X 87 ARG cc_start: 0.7373 (mtp180) cc_final: 0.7088 (mmp-170) REVERT: X 310 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: X 406 LEU cc_start: 0.8520 (tt) cc_final: 0.8233 (tp) REVERT: X 492 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: X 508 GLN cc_start: 0.7627 (tt0) cc_final: 0.7316 (tt0) REVERT: X 587 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.6871 (mtp85) REVERT: X 646 ASN cc_start: 0.7573 (m110) cc_final: 0.7262 (m-40) REVERT: X 672 MET cc_start: 0.7862 (mmp) cc_final: 0.7455 (mmm) REVERT: K 11 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6507 (mtt90) REVERT: K 44 LEU cc_start: 0.7945 (tp) cc_final: 0.7722 (tt) REVERT: K 204 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7033 (mt) REVERT: D 100 MET cc_start: 0.3694 (ttm) cc_final: 0.2020 (tmm) REVERT: P 83 GLN cc_start: 0.7329 (tp40) cc_final: 0.6974 (tt0) REVERT: P 167 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7094 (tp) REVERT: P 179 THR cc_start: 0.6695 (OUTLIER) cc_final: 0.6373 (p) REVERT: P 289 MET cc_start: 0.7670 (tpt) cc_final: 0.7233 (tpt) REVERT: P 543 ILE cc_start: 0.6968 (mt) cc_final: 0.6645 (mp) REVERT: P 581 THR cc_start: 0.8120 (m) cc_final: 0.7838 (m) REVERT: P 833 MET cc_start: 0.7639 (ttp) cc_final: 0.7430 (ttp) REVERT: T 124 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6998 (mm-40) REVERT: T 198 GLN cc_start: 0.7760 (pt0) cc_final: 0.7458 (tt0) REVERT: T 559 MET cc_start: 0.5509 (mmm) cc_final: 0.5172 (mmm) REVERT: S 191 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7328 (mp) REVERT: O 157 THR cc_start: 0.8472 (p) cc_final: 0.8221 (p) outliers start: 91 outliers final: 42 residues processed: 659 average time/residue: 0.7379 time to fit residues: 593.7924 Evaluate side-chains 648 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 594 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain X residue 8 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 492 GLN Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 317 LEU Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 239 GLN Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 336 VAL Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 55 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 76 optimal weight: 0.0980 chunk 62 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 181 optimal weight: 0.6980 chunk 461 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN W 18 GLN X 133 GLN X 151 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN L 117 ASN L 292 HIS P 339 GLN T 545 GLN S 122 ASN ** S 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.120299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.098985 restraints weight = 124046.929| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.51 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 39725 Z= 0.132 Angle : 0.533 10.805 54065 Z= 0.274 Chirality : 0.040 0.262 6408 Planarity : 0.004 0.046 6698 Dihedral : 5.926 105.733 5515 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.96 % Favored : 97.94 % Rotamer: Outliers : 2.00 % Allowed : 14.83 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.12), residues: 4925 helix: 2.12 (0.10), residues: 2868 sheet: 0.58 (0.27), residues: 346 loop : 0.19 (0.15), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 256 TYR 0.024 0.002 TYR A 455 PHE 0.038 0.002 PHE T 789 TRP 0.012 0.001 TRP P 81 HIS 0.021 0.001 HIS P 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (39723) covalent geometry : angle 0.53308 / 0.27 (54059) hydrogen bonds : bond 0.04288 / 2.96 ( 2377) hydrogen bonds : angle 4.56613 / 3.22 ( 6958) link_NAG-ASN : bond 0.00168 / 0.09 ( 2) link_NAG-ASN : angle 0.88965 / 0.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 612 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7028 (ttp-170) REVERT: A 92 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7167 (mp0) REVERT: A 451 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: X 87 ARG cc_start: 0.7401 (mtp180) cc_final: 0.7123 (mmp-170) REVERT: X 310 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: X 406 LEU cc_start: 0.8524 (tt) cc_final: 0.8255 (tp) REVERT: X 508 GLN cc_start: 0.7594 (tt0) cc_final: 0.7290 (tt0) REVERT: X 587 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.6882 (mtp85) REVERT: X 646 ASN cc_start: 0.7559 (m110) cc_final: 0.7297 (m-40) REVERT: X 672 MET cc_start: 0.7861 (mmp) cc_final: 0.7451 (mmm) REVERT: K 11 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6523 (mtt90) REVERT: K 204 ILE cc_start: 0.7344 (OUTLIER) cc_final: 0.7033 (mt) REVERT: D 100 MET cc_start: 0.3667 (ttm) cc_final: 0.2033 (tmm) REVERT: P 83 GLN cc_start: 0.7361 (tp40) cc_final: 0.7066 (tt0) REVERT: P 167 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7103 (tp) REVERT: P 179 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6351 (p) REVERT: P 289 MET cc_start: 0.7621 (tpt) cc_final: 0.7162 (tpt) REVERT: P 543 ILE cc_start: 0.7043 (mt) cc_final: 0.6716 (mp) REVERT: P 581 THR cc_start: 0.8116 (m) cc_final: 0.7814 (m) REVERT: P 615 LEU cc_start: 0.7193 (tm) cc_final: 0.6972 (tp) REVERT: P 679 PHE cc_start: 0.7596 (t80) cc_final: 0.7195 (t80) REVERT: P 833 MET cc_start: 0.7566 (ttp) cc_final: 0.7361 (ttp) REVERT: T 124 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6985 (mm-40) REVERT: T 198 GLN cc_start: 0.7793 (pt0) cc_final: 0.7486 (tt0) REVERT: T 559 MET cc_start: 0.5484 (mmm) cc_final: 0.5142 (mmm) REVERT: S 191 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7256 (mp) REVERT: O 157 THR cc_start: 0.8459 (p) cc_final: 0.8199 (p) REVERT: M 123 SER cc_start: 0.8482 (m) cc_final: 0.8240 (p) outliers start: 80 outliers final: 43 residues processed: 657 average time/residue: 0.7031 time to fit residues: 562.9971 Evaluate side-chains 653 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 599 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain W residue 18 GLN Chi-restraints excluded: chain X residue 8 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 100 ILE Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 657 SER Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 800 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 413 optimal weight: 0.7980 chunk 145 optimal weight: 0.4980 chunk 436 optimal weight: 4.9990 chunk 432 optimal weight: 3.9990 chunk 458 optimal weight: 4.9990 chunk 487 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 364 optimal weight: 0.0000 chunk 404 optimal weight: 0.5980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN X 133 GLN X 151 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN L 117 ASN L 292 HIS T 545 GLN S 122 ASN ** S 127 ASN ** 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 = 0.3539 r_free = 0.3539 target = 0.119698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097698 restraints weight = 99294.141| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.01 r_work: 0.2807 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 39725 Z= 0.151 Angle : 0.556 9.575 54065 Z= 0.284 Chirality : 0.040 0.261 6408 Planarity : 0.004 0.047 6698 Dihedral : 5.987 105.789 5515 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.02 % Favored : 97.88 % Rotamer: Outliers : 2.02 % Allowed : 15.07 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.12), residues: 4925 helix: 2.05 (0.10), residues: 2869 sheet: 0.58 (0.27), residues: 351 loop : 0.15 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 256 TYR 0.025 0.002 TYR A 455 PHE 0.042 0.002 PHE T 789 TRP 0.029 0.001 TRP K 220 HIS 0.006 0.001 HIS M 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (39723) covalent geometry : angle 0.55617 / 0.28 (54059) hydrogen bonds : bond 0.04496 / 3.10 ( 2377) hydrogen bonds : angle 4.61565 / 3.25 ( 6958) link_NAG-ASN : bond 0.00154 / 0.08 ( 2) link_NAG-ASN : angle 0.90644 / 0.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 600 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7370 (ttp-170) REVERT: A 451 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: X 87 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7404 (mmp-170) REVERT: X 310 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: X 406 LEU cc_start: 0.8734 (tt) cc_final: 0.8444 (tp) REVERT: X 508 GLN cc_start: 0.8156 (tt0) cc_final: 0.7895 (tt0) REVERT: X 587 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6952 (mtp85) REVERT: X 646 ASN cc_start: 0.7738 (m110) cc_final: 0.7468 (m-40) REVERT: X 672 MET cc_start: 0.8252 (mmp) cc_final: 0.7899 (mmm) REVERT: K 11 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6938 (mtt90) REVERT: K 16 TRP cc_start: 0.7138 (OUTLIER) cc_final: 0.6125 (t-100) REVERT: K 204 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7174 (mt) REVERT: L 164 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7894 (mttp) REVERT: D 100 MET cc_start: 0.3797 (ttm) cc_final: 0.1767 (tmm) REVERT: P 83 GLN cc_start: 0.7828 (tp40) cc_final: 0.7475 (tt0) REVERT: P 167 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7370 (tp) REVERT: P 179 THR cc_start: 0.7306 (OUTLIER) cc_final: 0.6952 (p) REVERT: P 289 MET cc_start: 0.8167 (tpt) cc_final: 0.7742 (tpt) REVERT: P 543 ILE cc_start: 0.7612 (mt) cc_final: 0.7401 (mp) REVERT: P 581 THR cc_start: 0.8560 (m) cc_final: 0.8316 (m) REVERT: P 679 PHE cc_start: 0.7611 (t80) cc_final: 0.7122 (t80) REVERT: T 74 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.8031 (ptm160) REVERT: T 124 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7970 (mm-40) REVERT: T 198 GLN cc_start: 0.8282 (pt0) cc_final: 0.8009 (tt0) REVERT: T 559 MET cc_start: 0.6072 (mmm) cc_final: 0.5671 (mmm) REVERT: S 191 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7436 (mp) REVERT: O 157 THR cc_start: 0.8559 (p) cc_final: 0.8321 (p) REVERT: M 123 SER cc_start: 0.8584 (m) cc_final: 0.8288 (p) outliers start: 81 outliers final: 46 residues processed: 643 average time/residue: 0.7333 time to fit residues: 575.3732 Evaluate side-chains 649 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 590 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain X residue 8 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 522 LEU Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 239 GLN Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain T residue 74 ARG Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 335 LEU Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 657 SER Chi-restraints excluded: chain T residue 696 MET Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 126 optimal weight: 0.9980 chunk 438 optimal weight: 0.7980 chunk 416 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 492 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 294 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN W 18 GLN X 151 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN L 117 ASN L 292 HIS T 545 GLN S 122 ASN ** S 127 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.119266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097838 restraints weight = 125195.125| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.53 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 39725 Z= 0.161 Angle : 0.572 10.067 54065 Z= 0.293 Chirality : 0.041 0.277 6408 Planarity : 0.004 0.047 6698 Dihedral : 6.051 105.769 5515 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.10 % Favored : 97.80 % Rotamer: Outliers : 1.75 % Allowed : 15.59 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.12), residues: 4925 helix: 2.00 (0.10), residues: 2866 sheet: 0.53 (0.27), residues: 351 loop : 0.12 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG T 344 TYR 0.027 0.002 TYR A 455 PHE 0.044 0.002 PHE T 789 TRP 0.026 0.001 TRP K 220 HIS 0.006 0.001 HIS M 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (39723) covalent geometry : angle 0.57202 / 0.29 (54059) hydrogen bonds : bond 0.04619 / 3.19 ( 2377) hydrogen bonds : angle 4.65617 / 3.28 ( 6958) link_NAG-ASN : bond 0.00144 / 0.07 ( 2) link_NAG-ASN : angle 0.92390 / 0.49 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 600 time to evaluate : 1.283 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7097 (ttp-170) REVERT: A 117 MET cc_start: 0.8454 (mtt) cc_final: 0.7854 (mtt) REVERT: A 451 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: A 454 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7964 (tptp) REVERT: X 87 ARG cc_start: 0.7404 (mtp180) cc_final: 0.7127 (mmp-170) REVERT: X 310 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: X 406 LEU cc_start: 0.8555 (tt) cc_final: 0.8285 (tp) REVERT: X 508 GLN cc_start: 0.7629 (tt0) cc_final: 0.7326 (tt0) REVERT: X 587 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6834 (mtp85) REVERT: X 599 GLU cc_start: 0.7211 (tm-30) cc_final: 0.7004 (tm-30) REVERT: X 672 MET cc_start: 0.7919 (mmp) cc_final: 0.7494 (mmm) REVERT: K 11 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6567 (mtt90) REVERT: K 16 TRP cc_start: 0.6564 (OUTLIER) cc_final: 0.5613 (t-100) REVERT: K 204 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.7066 (mt) REVERT: L 164 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7687 (mttp) REVERT: D 100 MET cc_start: 0.3793 (ttm) cc_final: 0.2120 (tmm) REVERT: P 83 GLN cc_start: 0.7297 (tp40) cc_final: 0.7048 (tt0) REVERT: P 167 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7175 (tp) REVERT: P 179 THR cc_start: 0.6697 (OUTLIER) cc_final: 0.6378 (p) REVERT: P 289 MET cc_start: 0.7631 (tpt) cc_final: 0.7234 (tpt) REVERT: P 543 ILE cc_start: 0.7120 (mt) cc_final: 0.6890 (mp) REVERT: P 679 PHE cc_start: 0.7544 (t80) cc_final: 0.7083 (t80) REVERT: T 74 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7440 (ptm160) REVERT: T 124 GLN cc_start: 0.7280 (OUTLIER) cc_final: 0.6981 (mm-40) REVERT: T 198 GLN cc_start: 0.7832 (pt0) cc_final: 0.7531 (tt0) REVERT: T 559 MET cc_start: 0.5496 (mmm) cc_final: 0.5162 (mmm) REVERT: S 191 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7214 (mp) REVERT: O 157 THR cc_start: 0.8416 (p) cc_final: 0.8165 (p) REVERT: M 123 SER cc_start: 0.8452 (m) cc_final: 0.8217 (p) outliers start: 70 outliers final: 47 residues processed: 639 average time/residue: 0.7089 time to fit residues: 551.7083 Evaluate side-chains 654 residues out of total 4133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 593 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ARG Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 454 LYS Chi-restraints excluded: chain X residue 8 LYS Chi-restraints excluded: chain X residue 143 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 379 THR Chi-restraints excluded: chain X residue 384 ASP Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 587 ARG Chi-restraints excluded: chain X residue 593 LYS Chi-restraints excluded: chain K residue 11 ARG Chi-restraints excluded: chain K residue 16 TRP Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain K residue 189 LYS Chi-restraints excluded: chain K residue 204 ILE Chi-restraints excluded: chain K residue 223 VAL Chi-restraints excluded: chain K residue 236 ASN Chi-restraints excluded: chain K residue 249 VAL Chi-restraints excluded: chain K residue 290 SER Chi-restraints excluded: chain K residue 327 VAL Chi-restraints excluded: chain K residue 386 LEU Chi-restraints excluded: chain L residue 164 LYS Chi-restraints excluded: chain L residue 266 LYS Chi-restraints excluded: chain Q residue 10 ILE Chi-restraints excluded: chain Q residue 283 VAL Chi-restraints excluded: chain Q residue 408 THR Chi-restraints excluded: chain N residue 81 VAL Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain P residue 179 THR Chi-restraints excluded: chain P residue 260 VAL Chi-restraints excluded: chain P residue 336 VAL Chi-restraints excluded: chain P residue 462 VAL Chi-restraints excluded: chain P residue 500 LEU Chi-restraints excluded: chain P residue 528 ILE Chi-restraints excluded: chain P residue 560 VAL Chi-restraints excluded: chain P residue 601 LEU Chi-restraints excluded: chain P residue 640 VAL Chi-restraints excluded: chain P residue 646 ARG Chi-restraints excluded: chain P residue 673 LEU Chi-restraints excluded: chain T residue 74 ARG Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain T residue 124 GLN Chi-restraints excluded: chain T residue 216 ILE Chi-restraints excluded: chain T residue 551 LYS Chi-restraints excluded: chain T residue 560 VAL Chi-restraints excluded: chain T residue 602 ARG Chi-restraints excluded: chain T residue 639 LYS Chi-restraints excluded: chain T residue 696 MET Chi-restraints excluded: chain T residue 729 VAL Chi-restraints excluded: chain T residue 800 LEU Chi-restraints excluded: chain T residue 812 LEU Chi-restraints excluded: chain S residue 191 ILE Chi-restraints excluded: chain O residue 9 LEU Chi-restraints excluded: chain O residue 115 ILE Chi-restraints excluded: chain O residue 124 LEU Chi-restraints excluded: chain R residue 42 ASN Chi-restraints excluded: chain R residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 477 optimal weight: 2.9990 chunk 469 optimal weight: 0.5980 chunk 299 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 482 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 458 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 427 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN A 138 ASN A 165 ASN W 18 GLN X 151 ASN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN X 602 GLN X 646 ASN L 292 HIS L 395 ASN T 545 GLN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096528 restraints weight = 127092.119| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.48 r_work: 0.2740 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 39725 Z= 0.251 Angle : 0.665 10.373 54065 Z= 0.341 Chirality : 0.045 0.312 6408 Planarity : 0.005 0.068 6698 Dihedral : 6.414 107.308 5515 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.58 % Rotamer: Outliers : 1.95 % Allowed : 15.59 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.12), residues: 4925 helix: 1.69 (0.10), residues: 2863 sheet: 0.48 (0.27), residues: 349 loop : -0.05 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG T 344 TYR 0.033 0.003 TYR A 455 PHE 0.048 0.003 PHE X 639 TRP 0.048 0.002 TRP K 220 HIS 0.007 0.002 HIS Q 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (39723) covalent geometry : angle 0.66534 / 0.34 (54059) hydrogen bonds : bond 0.05460 / 3.77 ( 2377) hydrogen bonds : angle 4.87119 / 3.43 ( 6958) link_NAG-ASN : bond 0.00100 / 0.05 ( 2) link_NAG-ASN : angle 0.99605 / 0.53 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13309.25 seconds wall clock time: 227 minutes 42.71 seconds (13662.71 seconds total)