Starting phenix.real_space_refine on Sat Mar 7 10:17:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796.map" model { file = "/net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dop_30796/03_2026/7dop_30796_neut.cif" } resolution = 2.38 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= 0.001 sd= 0.069 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 Zn 12 6.06 5 S 348 5.16 5 C 26400 2.51 5 N 7200 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41700 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3474 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 446, 3468 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 424} Chain breaks: 4 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 3533 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 973 SG CYS A 134 118.569 187.968 30.521 1.00 95.42 S ATOM 1025 SG CYS A 141 115.102 189.644 31.353 1.00 89.69 S Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 5.13, per 1000 atoms: 0.12 Number of scatterers: 41700 At special positions: 0 Unit cell: (205.062, 205.062, 95.238, 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) Zn 12 29.99 S 348 16.00 O 7740 8.00 N 7200 7.00 C 26400 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 Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10176 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 72 sheets defined 35.7% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 335 through 342 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU B 346 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 404 Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 removed outlier: 3.529A pdb=" N GLN C 364 " --> pdb=" O VAL C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 348 " --> pdb=" O ILE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN D 364 " --> pdb=" O VAL D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 404 Processing helix chain 'D' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU D 471 " --> pdb=" O ARG D 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D 472 " --> pdb=" O ILE D 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 Processing helix chain 'E' and resid 67 through 72 removed outlier: 4.259A pdb=" N ARG E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU E 346 " --> pdb=" O THR E 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN E 364 " --> pdb=" O VAL E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 Processing helix chain 'E' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU E 471 " --> pdb=" O ARG E 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 54 Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA F 101 " --> pdb=" O ALA F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 193 through 195 No H-bonds generated for 'chain 'F' and resid 193 through 195' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 removed outlier: 3.527A pdb=" N GLN F 364 " --> pdb=" O VAL F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 404 Processing helix chain 'F' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU F 471 " --> pdb=" O ARG F 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 472 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.261A pdb=" N ARG G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN G 364 " --> pdb=" O VAL G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 472 " --> pdb=" O ILE G 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 54 Processing helix chain 'H' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 335 through 342 Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN H 364 " --> pdb=" O VAL H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 404 Processing helix chain 'H' and resid 461 through 473 removed outlier: 3.641A pdb=" N LEU H 471 " --> pdb=" O ARG H 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU H 472 " --> pdb=" O ILE H 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 54 Processing helix chain 'I' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN I 364 " --> pdb=" O VAL I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU I 471 " --> pdb=" O ARG I 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU I 472 " --> pdb=" O ILE I 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 54 Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG J 71 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA J 101 " --> pdb=" O ALA J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 342 Processing helix chain 'J' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU J 346 " --> pdb=" O THR J 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR J 348 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN J 364 " --> pdb=" O VAL J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 404 Processing helix chain 'J' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU J 471 " --> pdb=" O ARG J 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU J 472 " --> pdb=" O ILE J 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 3.725A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 54 Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 removed outlier: 3.586A pdb=" N ALA K 101 " --> pdb=" O ALA K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 342 Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN K 364 " --> pdb=" O VAL K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 Processing helix chain 'K' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU K 471 " --> pdb=" O ARG K 467 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 472 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 22 removed outlier: 3.724A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 Processing helix chain 'L' and resid 67 through 72 removed outlier: 4.260A pdb=" N ARG L 71 " --> pdb=" O ALA L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 removed outlier: 3.587A pdb=" N ALA L 101 " --> pdb=" O ALA L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.658A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR L 348 " --> pdb=" O ILE L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 removed outlier: 3.528A pdb=" N GLN L 364 " --> pdb=" O VAL L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 404 Processing helix chain 'L' and resid 461 through 473 removed outlier: 3.640A pdb=" N LEU L 471 " --> pdb=" O ARG L 467 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 472 " --> pdb=" O ILE L 468 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 251 removed outlier: 3.648A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 189 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR A 333 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA A 191 " --> pdb=" O TYR A 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA7, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA8, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 63 Processing sheet with id=AB1, first strand: chain 'B' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 281 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL B 287 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE B 447 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS B 265 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 303 through 307 Processing sheet with id=AB4, first strand: chain 'B' and resid 422 through 423 Processing sheet with id=AB5, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 246 through 251 removed outlier: 3.648A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AC1, first strand: chain 'C' and resid 422 through 423 Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 60 through 63 Processing sheet with id=AC4, first strand: chain 'D' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL D 287 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE D 447 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS D 265 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 303 through 307 Processing sheet with id=AC7, first strand: chain 'D' and resid 422 through 423 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 60 through 63 Processing sheet with id=AD1, first strand: chain 'E' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE E 447 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS E 265 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AD4, first strand: chain 'E' and resid 422 through 423 Processing sheet with id=AD5, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'F' and resid 60 through 63 Processing sheet with id=AD7, first strand: chain 'F' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE F 447 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS F 265 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA F 189 " --> pdb=" O CYS F 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR F 333 " --> pdb=" O ALA F 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA F 191 " --> pdb=" O TYR F 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 303 through 307 Processing sheet with id=AE1, first strand: chain 'F' and resid 422 through 423 Processing sheet with id=AE2, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'G' and resid 60 through 63 Processing sheet with id=AE4, first strand: chain 'G' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AE7, first strand: chain 'G' and resid 422 through 423 Processing sheet with id=AE8, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE9, first strand: chain 'H' and resid 60 through 63 Processing sheet with id=AF1, first strand: chain 'H' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 303 through 307 Processing sheet with id=AF4, first strand: chain 'H' and resid 421 through 423 removed outlier: 4.003A pdb=" N TRP H 421 " --> pdb=" O SER I 226 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'I' and resid 60 through 63 Processing sheet with id=AF7, first strand: chain 'I' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AG1, first strand: chain 'I' and resid 421 through 423 removed outlier: 3.921A pdb=" N TRP I 421 " --> pdb=" O SER K 226 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AG3, first strand: chain 'J' and resid 60 through 63 Processing sheet with id=AG4, first strand: chain 'J' and resid 147 through 151 removed outlier: 6.612A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE J 447 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS J 265 " --> pdb=" O PHE J 447 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA J 189 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR J 333 " --> pdb=" O ALA J 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA J 191 " --> pdb=" O TYR J 333 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 225 through 226 removed outlier: 3.931A pdb=" N TRP L 421 " --> pdb=" O SER J 226 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 303 through 307 Processing sheet with id=AG8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AG9, first strand: chain 'K' and resid 60 through 63 Processing sheet with id=AH1, first strand: chain 'K' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AH4, first strand: chain 'K' and resid 422 through 423 Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AH6, first strand: chain 'L' and resid 60 through 63 Processing sheet with id=AH7, first strand: chain 'L' and resid 147 through 151 removed outlier: 6.613A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N PHE L 447 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS L 265 " --> pdb=" O PHE L 447 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 246 through 251 removed outlier: 3.647A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA L 189 " --> pdb=" O CYS L 331 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N TYR L 333 " --> pdb=" O ALA L 189 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ALA L 191 " --> pdb=" O TYR L 333 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 303 through 307 1825 hydrogen bonds defined for protein. 5262 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: 9.95 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13419 1.34 - 1.46: 9406 1.46 - 1.58: 19223 1.58 - 1.71: 0 1.71 - 1.83: 516 Bond restraints: 42564 Sorted by residual: bond pdb=" CB GLU F 353 " pdb=" CG GLU F 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.46e+00 bond pdb=" CB GLU E 353 " pdb=" CG GLU E 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CB GLU A 353 " pdb=" CG GLU A 353 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.45e+00 bond pdb=" CB GLU C 353 " pdb=" CG GLU C 353 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.42e+00 bond pdb=" CB GLU K 353 " pdb=" CG GLU K 353 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.42e+00 ... (remaining 42559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 56618 2.25 - 4.51: 853 4.51 - 6.76: 129 6.76 - 9.01: 36 9.01 - 11.26: 24 Bond angle restraints: 57660 Sorted by residual: angle pdb=" CA GLU L 353 " pdb=" CB GLU L 353 " pdb=" CG GLU L 353 " ideal model delta sigma weight residual 114.10 123.57 -9.47 2.00e+00 2.50e-01 2.24e+01 angle pdb=" CA GLU H 353 " pdb=" CB GLU H 353 " pdb=" CG GLU H 353 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CA GLU I 353 " pdb=" CB GLU I 353 " pdb=" CG GLU I 353 " ideal model delta sigma weight residual 114.10 123.54 -9.44 2.00e+00 2.50e-01 2.23e+01 angle pdb=" CA GLU G 353 " pdb=" CB GLU G 353 " pdb=" CG GLU G 353 " ideal model delta sigma weight residual 114.10 123.53 -9.43 2.00e+00 2.50e-01 2.22e+01 angle pdb=" CA GLU B 353 " pdb=" CB GLU B 353 " pdb=" CG GLU B 353 " ideal model delta sigma weight residual 114.10 123.52 -9.42 2.00e+00 2.50e-01 2.22e+01 ... (remaining 57655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 22370 17.58 - 35.16: 2590 35.16 - 52.74: 672 52.74 - 70.32: 144 70.32 - 87.90: 24 Dihedral angle restraints: 25800 sinusoidal: 10092 harmonic: 15708 Sorted by residual: dihedral pdb=" CA TYR K 192 " pdb=" C TYR K 192 " pdb=" N PRO K 193 " pdb=" CA PRO K 193 " ideal model delta harmonic sigma weight residual -180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR H 192 " pdb=" C TYR H 192 " pdb=" N PRO H 193 " pdb=" CA PRO H 193 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR C 192 " pdb=" C TYR C 192 " pdb=" N PRO C 193 " pdb=" CA PRO C 193 " ideal model delta harmonic sigma weight residual 180.00 -161.23 -18.77 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 25797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3254 0.031 - 0.063: 1980 0.063 - 0.094: 816 0.094 - 0.125: 378 0.125 - 0.157: 124 Chirality restraints: 6552 Sorted by residual: chirality pdb=" CA ARG G 411 " pdb=" N ARG G 411 " pdb=" C ARG G 411 " pdb=" CB ARG G 411 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.14e-01 chirality pdb=" CA ARG I 411 " pdb=" N ARG I 411 " pdb=" C ARG I 411 " pdb=" CB ARG I 411 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ARG F 411 " pdb=" N ARG F 411 " pdb=" C ARG F 411 " pdb=" CB ARG F 411 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.97e-01 ... (remaining 6549 not shown) Planarity restraints: 7308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 89 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO D 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO D 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 89 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO C 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 90 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 90 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 89 " -0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO E 90 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 90 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 90 " -0.026 5.00e-02 4.00e+02 ... (remaining 7305 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 135 2.50 - 3.10: 26072 3.10 - 3.70: 58248 3.70 - 4.30: 88425 4.30 - 4.90: 147238 Nonbonded interactions: 320118 Sorted by model distance: nonbonded pdb=" OE2 GLU L 129 " pdb="ZN ZN L1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU C 129 " pdb="ZN ZN C1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU E 129 " pdb="ZN ZN E1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU J 129 " pdb="ZN ZN J1001 " model vdw 1.895 2.230 nonbonded pdb=" OE2 GLU D 129 " pdb="ZN ZN D1001 " model vdw 1.895 2.230 ... (remaining 320113 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.50 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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.910 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.005 0.056 42600 Z= 0.224 Angle : 0.781 11.264 57660 Z= 0.427 Chirality : 0.051 0.157 6552 Planarity : 0.005 0.046 7308 Dihedral : 16.240 87.904 15624 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.21 % Allowed : 16.47 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.11), residues: 5268 helix: -0.53 (0.13), residues: 1644 sheet: -0.93 (0.14), residues: 1212 loop : -1.86 (0.10), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 41 TYR 0.015 0.002 TYR B 248 PHE 0.028 0.003 PHE H 183 TRP 0.013 0.002 TRP A 175 HIS 0.006 0.002 HIS K 164 Details of bonding type rmsd covalent geometry : bond 0.00512 (42564) covalent geometry : angle 0.78112 (57660) hydrogen bonds : bond 0.28363 ( 1825) hydrogen bonds : angle 7.45020 ( 5262) metal coordination : bond 0.00393 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 370 time to evaluate : 1.535 Fit side-chains REVERT: A 228 MET cc_start: 0.4930 (ttt) cc_final: 0.4315 (tpp) REVERT: A 285 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 285 TYR cc_start: 0.8568 (OUTLIER) cc_final: 0.8149 (t80) REVERT: C 285 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.8195 (t80) REVERT: D 30 ARG cc_start: 0.4327 (OUTLIER) cc_final: 0.4101 (ptm-80) REVERT: E 285 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7905 (t80) REVERT: G 228 MET cc_start: 0.4925 (ttt) cc_final: 0.4441 (tpp) REVERT: H 228 MET cc_start: 0.5014 (ttt) cc_final: 0.4374 (tpt) REVERT: H 285 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.7838 (t80) REVERT: I 285 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7900 (t80) REVERT: J 285 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8055 (t80) REVERT: K 41 ARG cc_start: 0.5435 (ttp-110) cc_final: 0.5225 (ttp-110) REVERT: K 110 ARG cc_start: 0.5100 (mtt90) cc_final: 0.4420 (mtt-85) REVERT: K 228 MET cc_start: 0.5206 (ttt) cc_final: 0.4447 (tpp) REVERT: K 285 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.7867 (t80) outliers start: 99 outliers final: 10 residues processed: 425 average time/residue: 0.7867 time to fit residues: 401.9429 Evaluate side-chains 357 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 338 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 30 ARG Chi-restraints excluded: chain E residue 208 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 353 GLU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 472 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 0.0970 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 10.0000 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN J 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.209326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156405 restraints weight = 99025.632| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 6.10 r_work: 0.3158 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 42600 Z= 0.135 Angle : 0.607 13.458 57660 Z= 0.324 Chirality : 0.045 0.131 6552 Planarity : 0.005 0.046 7308 Dihedral : 5.562 110.403 5864 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.47 % Allowed : 17.71 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.11), residues: 5268 helix: 0.93 (0.13), residues: 1668 sheet: 0.22 (0.15), residues: 1152 loop : -1.64 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 41 TYR 0.011 0.001 TYR K 248 PHE 0.013 0.001 PHE I 423 TRP 0.009 0.001 TRP H 421 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00277 (42564) covalent geometry : angle 0.60690 (57660) hydrogen bonds : bond 0.05702 ( 1825) hydrogen bonds : angle 4.93263 ( 5262) metal coordination : bond 0.00370 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 353 time to evaluate : 1.503 Fit side-chains REVERT: A 72 MET cc_start: 0.5600 (ttp) cc_final: 0.4945 (ttp) REVERT: A 73 MET cc_start: 0.6136 (mmm) cc_final: 0.5776 (tmm) REVERT: A 228 MET cc_start: 0.5161 (ttt) cc_final: 0.4414 (tpp) REVERT: A 285 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8465 (t80) REVERT: B 41 ARG cc_start: 0.5978 (OUTLIER) cc_final: 0.5772 (ttp-110) REVERT: B 222 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.5501 (ttm-80) REVERT: B 285 TYR cc_start: 0.8837 (OUTLIER) cc_final: 0.8495 (t80) REVERT: B 292 MET cc_start: 0.7050 (mtm) cc_final: 0.6602 (mtp) REVERT: B 402 MET cc_start: 0.7937 (mtm) cc_final: 0.7668 (mtt) REVERT: C 41 ARG cc_start: 0.5890 (ttp-110) cc_final: 0.5659 (ttp-110) REVERT: C 285 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.8456 (t80) REVERT: D 285 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8535 (t80) REVERT: D 314 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8530 (ttt) REVERT: D 342 MET cc_start: 0.8606 (mmm) cc_final: 0.8291 (mmm) REVERT: E 73 MET cc_start: 0.6011 (mmm) cc_final: 0.5686 (tmm) REVERT: E 285 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8414 (t80) REVERT: F 285 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8408 (t80) REVERT: G 228 MET cc_start: 0.4971 (ttt) cc_final: 0.4521 (tpp) REVERT: G 285 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8462 (t80) REVERT: G 292 MET cc_start: 0.6915 (mtp) cc_final: 0.6649 (mtm) REVERT: G 314 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8607 (ttt) REVERT: H 285 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8374 (t80) REVERT: H 402 MET cc_start: 0.7998 (mtm) cc_final: 0.7723 (mtt) REVERT: I 73 MET cc_start: 0.6085 (tmm) cc_final: 0.5799 (tpt) REVERT: I 285 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8440 (t80) REVERT: I 389 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: J 285 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8493 (t80) REVERT: J 389 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: K 41 ARG cc_start: 0.6212 (ttp-110) cc_final: 0.5994 (ttp-110) REVERT: K 285 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8402 (t80) REVERT: K 402 MET cc_start: 0.7723 (mtm) cc_final: 0.7506 (mtt) REVERT: L 24 MET cc_start: 0.5871 (pmt) cc_final: 0.5584 (pmt) REVERT: L 30 ARG cc_start: 0.4128 (OUTLIER) cc_final: 0.3923 (ptp-110) REVERT: L 285 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8504 (t80) REVERT: L 402 MET cc_start: 0.7882 (mtm) cc_final: 0.7631 (mtt) outliers start: 66 outliers final: 17 residues processed: 407 average time/residue: 0.7274 time to fit residues: 361.6124 Evaluate side-chains 375 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 314 MET Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 314 MET Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 229 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 384 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 392 optimal weight: 6.9990 chunk 459 optimal weight: 3.9990 chunk 319 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.203793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.162587 restraints weight = 83785.341| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.26 r_work: 0.3183 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 42600 Z= 0.277 Angle : 0.811 12.206 57660 Z= 0.442 Chirality : 0.054 0.175 6552 Planarity : 0.006 0.050 7308 Dihedral : 5.684 58.190 5844 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.28 % Allowed : 15.62 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.11), residues: 5268 helix: 1.06 (0.13), residues: 1656 sheet: 0.34 (0.15), residues: 1140 loop : -1.76 (0.10), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 252 TYR 0.020 0.003 TYR B 150 PHE 0.031 0.003 PHE E 183 TRP 0.019 0.003 TRP F 175 HIS 0.007 0.002 HIS K 307 Details of bonding type rmsd covalent geometry : bond 0.00605 (42564) covalent geometry : angle 0.81120 (57660) hydrogen bonds : bond 0.08538 ( 1825) hydrogen bonds : angle 5.08389 ( 5262) metal coordination : bond 0.00652 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 312 time to evaluate : 1.512 Fit side-chains REVERT: A 228 MET cc_start: 0.5158 (ttt) cc_final: 0.4522 (tpp) REVERT: B 99 LYS cc_start: 0.6776 (OUTLIER) cc_final: 0.6270 (mptt) REVERT: B 285 TYR cc_start: 0.8937 (OUTLIER) cc_final: 0.8482 (t80) REVERT: B 292 MET cc_start: 0.7270 (mtm) cc_final: 0.6804 (mtp) REVERT: B 389 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: C 99 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6433 (mptt) REVERT: C 285 TYR cc_start: 0.8884 (OUTLIER) cc_final: 0.8324 (t80) REVERT: C 389 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.8076 (tm-30) REVERT: D 99 LYS cc_start: 0.7051 (OUTLIER) cc_final: 0.6454 (mptt) REVERT: D 285 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8596 (t80) REVERT: E 99 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6563 (mptt) REVERT: E 285 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.8422 (t80) REVERT: E 389 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8303 (tm-30) REVERT: F 99 LYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6451 (mptt) REVERT: F 202 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8347 (mm-30) REVERT: F 285 TYR cc_start: 0.8856 (OUTLIER) cc_final: 0.8485 (t80) REVERT: F 389 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: G 72 MET cc_start: 0.5741 (ttp) cc_final: 0.5271 (ttp) REVERT: G 99 LYS cc_start: 0.6818 (OUTLIER) cc_final: 0.6269 (mptt) REVERT: G 228 MET cc_start: 0.4951 (ttt) cc_final: 0.4582 (tpp) REVERT: G 285 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.8579 (t80) REVERT: G 292 MET cc_start: 0.7207 (mtp) cc_final: 0.6941 (mtm) REVERT: H 99 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6310 (mptt) REVERT: H 285 TYR cc_start: 0.8931 (OUTLIER) cc_final: 0.8420 (t80) REVERT: H 389 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: I 285 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.8328 (t80) REVERT: I 389 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: J 285 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8372 (t80) REVERT: J 389 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: L 24 MET cc_start: 0.6151 (pmt) cc_final: 0.5803 (pmt) REVERT: L 285 TYR cc_start: 0.8911 (OUTLIER) cc_final: 0.8563 (t80) REVERT: L 389 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8280 (tm-30) outliers start: 147 outliers final: 72 residues processed: 437 average time/residue: 0.7177 time to fit residues: 383.0427 Evaluate side-chains 408 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 310 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 419 CYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 419 CYS Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 24 MET Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 202 GLU Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 419 CYS Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 24 MET Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 419 CYS Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 24 MET Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 348 THR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain J residue 419 CYS Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 419 CYS Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 348 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 419 CYS Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 283 optimal weight: 0.6980 chunk 275 optimal weight: 20.0000 chunk 314 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 chunk 458 optimal weight: 0.6980 chunk 253 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 0.8980 chunk 324 optimal weight: 7.9990 chunk 492 optimal weight: 10.0000 chunk 257 optimal weight: 0.7980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.207459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.152802 restraints weight = 109618.240| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 6.53 r_work: 0.3132 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42600 Z= 0.146 Angle : 0.622 13.270 57660 Z= 0.331 Chirality : 0.046 0.152 6552 Planarity : 0.005 0.047 7308 Dihedral : 5.207 59.952 5844 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.47 % Allowed : 16.15 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.11), residues: 5268 helix: 1.56 (0.14), residues: 1668 sheet: 0.43 (0.15), residues: 1152 loop : -1.62 (0.10), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 110 TYR 0.012 0.001 TYR A 248 PHE 0.017 0.002 PHE I 423 TRP 0.010 0.002 TRP C 175 HIS 0.003 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00302 (42564) covalent geometry : angle 0.62206 (57660) hydrogen bonds : bond 0.05457 ( 1825) hydrogen bonds : angle 4.65297 ( 5262) metal coordination : bond 0.00403 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 337 time to evaluate : 1.536 Fit side-chains REVERT: B 292 MET cc_start: 0.7066 (mtm) cc_final: 0.6676 (mtp) REVERT: B 389 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8262 (tm-30) REVERT: B 402 MET cc_start: 0.8087 (mtm) cc_final: 0.7779 (mtt) REVERT: C 73 MET cc_start: 0.6365 (tmt) cc_final: 0.6027 (tpt) REVERT: C 99 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6112 (mptt) REVERT: C 389 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: D 285 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8562 (t80) REVERT: E 99 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6138 (mptt) REVERT: E 389 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: E 402 MET cc_start: 0.8073 (mtm) cc_final: 0.7771 (mtt) REVERT: F 99 LYS cc_start: 0.6539 (OUTLIER) cc_final: 0.6086 (mptt) REVERT: F 285 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.8470 (t80) REVERT: F 389 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: G 285 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.8593 (t80) REVERT: G 292 MET cc_start: 0.6967 (mtp) cc_final: 0.6698 (mtm) REVERT: H 389 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8283 (tm-30) REVERT: I 389 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: J 389 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7993 (tm-30) REVERT: L 24 MET cc_start: 0.6156 (pmt) cc_final: 0.5736 (pmt) REVERT: L 285 TYR cc_start: 0.8823 (OUTLIER) cc_final: 0.8444 (t80) REVERT: L 292 MET cc_start: 0.6929 (mtp) cc_final: 0.6690 (mtm) REVERT: L 389 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8263 (tm-30) REVERT: L 402 MET cc_start: 0.8128 (mtm) cc_final: 0.7823 (mtt) outliers start: 111 outliers final: 45 residues processed: 434 average time/residue: 0.7395 time to fit residues: 390.0841 Evaluate side-chains 380 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 30 ARG Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 414 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 393 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 367 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 276 optimal weight: 7.9990 chunk 431 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.204631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.151203 restraints weight = 95588.711| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 5.55 r_work: 0.3091 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 42600 Z= 0.206 Angle : 0.705 13.121 57660 Z= 0.380 Chirality : 0.050 0.164 6552 Planarity : 0.005 0.049 7308 Dihedral : 5.404 59.633 5842 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.72 % Allowed : 16.18 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.11), residues: 5268 helix: 1.54 (0.14), residues: 1668 sheet: 0.46 (0.15), residues: 1140 loop : -1.72 (0.10), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 110 TYR 0.017 0.002 TYR L 150 PHE 0.024 0.002 PHE H 183 TRP 0.015 0.002 TRP F 175 HIS 0.005 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00439 (42564) covalent geometry : angle 0.70458 (57660) hydrogen bonds : bond 0.07067 ( 1825) hydrogen bonds : angle 4.78762 ( 5262) metal coordination : bond 0.00463 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 316 time to evaluate : 1.267 Fit side-chains REVERT: B 285 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8404 (t80) REVERT: B 292 MET cc_start: 0.7068 (mtm) cc_final: 0.6681 (mtp) REVERT: B 389 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8365 (tm-30) REVERT: C 99 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5997 (mptt) REVERT: C 389 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: D 285 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.8551 (t80) REVERT: E 73 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5800 (tmm) REVERT: E 99 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6077 (mptt) REVERT: E 285 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8384 (t80) REVERT: E 389 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: F 99 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6047 (mptt) REVERT: F 285 TYR cc_start: 0.8848 (OUTLIER) cc_final: 0.8513 (t80) REVERT: F 389 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: G 285 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8572 (t80) REVERT: G 292 MET cc_start: 0.6999 (mtp) cc_final: 0.6723 (mtm) REVERT: H 285 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8374 (t80) REVERT: H 389 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: I 389 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: J 389 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: L 24 MET cc_start: 0.6112 (pmt) cc_final: 0.5688 (pmt) REVERT: L 285 TYR cc_start: 0.8899 (OUTLIER) cc_final: 0.8538 (t80) REVERT: L 292 MET cc_start: 0.7029 (mtp) cc_final: 0.6738 (mtm) REVERT: L 389 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8366 (tm-30) outliers start: 122 outliers final: 73 residues processed: 417 average time/residue: 0.6910 time to fit residues: 352.7023 Evaluate side-chains 403 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 311 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ARG Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 419 CYS Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 419 CYS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 99 LYS Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain F residue 402 MET Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 214 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain I residue 402 MET Chi-restraints excluded: chain I residue 472 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 402 MET Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 18 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 214 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 419 CYS Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 228 MET Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 419 CYS Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 19 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 411 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 336 optimal weight: 1.9990 chunk 344 optimal weight: 0.5980 chunk 448 optimal weight: 10.0000 chunk 438 optimal weight: 0.0970 chunk 376 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.209542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.158118 restraints weight = 98862.409| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 5.58 r_work: 0.3175 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 42600 Z= 0.114 Angle : 0.541 11.487 57660 Z= 0.286 Chirality : 0.044 0.157 6552 Planarity : 0.005 0.046 7308 Dihedral : 4.843 59.534 5842 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.03 % Allowed : 17.18 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.11), residues: 5268 helix: 1.89 (0.14), residues: 1680 sheet: 0.53 (0.15), residues: 1200 loop : -1.64 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.010 0.001 TYR B 382 PHE 0.018 0.001 PHE I 423 TRP 0.008 0.001 TRP D 421 HIS 0.002 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00234 (42564) covalent geometry : angle 0.54097 (57660) hydrogen bonds : bond 0.04100 ( 1825) hydrogen bonds : angle 4.36995 ( 5262) metal coordination : bond 0.00320 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 344 time to evaluate : 1.568 Fit side-chains REVERT: B 389 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: B 402 MET cc_start: 0.7754 (mtm) cc_final: 0.7478 (mtt) REVERT: C 389 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8104 (tt0) REVERT: D 285 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8513 (t80) REVERT: E 73 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5710 (tmt) REVERT: E 389 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: E 402 MET cc_start: 0.7735 (mtm) cc_final: 0.7460 (mtt) REVERT: F 285 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8419 (t80) REVERT: F 353 GLU cc_start: 0.7756 (mp0) cc_final: 0.7477 (mp0) REVERT: F 389 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: G 73 MET cc_start: 0.5964 (mmt) cc_final: 0.5728 (tmm) REVERT: G 285 TYR cc_start: 0.8722 (OUTLIER) cc_final: 0.8496 (t80) REVERT: G 292 MET cc_start: 0.6960 (mtp) cc_final: 0.6694 (mtm) REVERT: H 389 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: I 389 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: J 389 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: K 73 MET cc_start: 0.5534 (tpp) cc_final: 0.5231 (tmm) REVERT: L 24 MET cc_start: 0.6114 (pmt) cc_final: 0.5627 (pmt) REVERT: L 30 ARG cc_start: 0.4304 (OUTLIER) cc_final: 0.4097 (ptp-110) REVERT: L 41 ARG cc_start: 0.6234 (ttp-110) cc_final: 0.6016 (ttp-110) REVERT: L 285 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8376 (t80) REVERT: L 389 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: L 402 MET cc_start: 0.7754 (mtm) cc_final: 0.7484 (mtt) outliers start: 91 outliers final: 44 residues processed: 425 average time/residue: 0.6740 time to fit residues: 353.3066 Evaluate side-chains 394 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 336 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 483 optimal weight: 3.9990 chunk 263 optimal weight: 0.8980 chunk 425 optimal weight: 2.9990 chunk 358 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 359 optimal weight: 6.9990 chunk 399 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 237 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 441 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.209770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.169516 restraints weight = 93348.366| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.45 r_work: 0.3252 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42600 Z= 0.110 Angle : 0.526 10.061 57660 Z= 0.275 Chirality : 0.043 0.155 6552 Planarity : 0.005 0.044 7308 Dihedral : 4.593 59.939 5836 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.87 % Allowed : 17.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.12), residues: 5268 helix: 2.18 (0.14), residues: 1680 sheet: 0.67 (0.15), residues: 1200 loop : -1.65 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.010 0.001 TYR K 248 PHE 0.021 0.001 PHE I 423 TRP 0.008 0.001 TRP F 421 HIS 0.002 0.001 HIS L 164 Details of bonding type rmsd covalent geometry : bond 0.00229 (42564) covalent geometry : angle 0.52621 (57660) hydrogen bonds : bond 0.04006 ( 1825) hydrogen bonds : angle 4.20973 ( 5262) metal coordination : bond 0.00308 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 361 time to evaluate : 1.409 Fit side-chains REVERT: B 389 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: B 402 MET cc_start: 0.7696 (mtm) cc_final: 0.7412 (mtt) REVERT: C 389 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: D 41 ARG cc_start: 0.6223 (ttp80) cc_final: 0.5748 (ttp-110) REVERT: D 285 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8455 (t80) REVERT: E 389 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: E 402 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7416 (mtt) REVERT: F 285 TYR cc_start: 0.8680 (OUTLIER) cc_final: 0.8405 (t80) REVERT: F 389 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: G 285 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8471 (t80) REVERT: G 292 MET cc_start: 0.6971 (mtp) cc_final: 0.6666 (mtm) REVERT: H 389 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: J 389 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: K 73 MET cc_start: 0.5756 (tpp) cc_final: 0.5501 (tmt) REVERT: L 24 MET cc_start: 0.6143 (pmt) cc_final: 0.5649 (pmt) REVERT: L 285 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.8384 (t80) REVERT: L 389 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8174 (tm-30) REVERT: L 402 MET cc_start: 0.7702 (mtm) cc_final: 0.7419 (mtt) outliers start: 84 outliers final: 52 residues processed: 440 average time/residue: 0.6841 time to fit residues: 368.9683 Evaluate side-chains 417 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 353 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 389 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 222 ARG Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 417 optimal weight: 0.9980 chunk 310 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 470 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 292 optimal weight: 0.8980 chunk 440 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 211 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 312 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 GLN G 165 GLN K 165 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.209292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169899 restraints weight = 91631.762| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 2.31 r_work: 0.3253 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 42600 Z= 0.115 Angle : 0.546 14.243 57660 Z= 0.283 Chirality : 0.044 0.166 6552 Planarity : 0.005 0.044 7308 Dihedral : 4.610 59.913 5836 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.78 % Allowed : 17.85 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.11), residues: 5268 helix: 2.27 (0.14), residues: 1680 sheet: 0.74 (0.15), residues: 1152 loop : -1.55 (0.10), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.010 0.001 TYR G 248 PHE 0.013 0.001 PHE I 183 TRP 0.009 0.001 TRP F 421 HIS 0.002 0.001 HIS L 164 Details of bonding type rmsd covalent geometry : bond 0.00241 (42564) covalent geometry : angle 0.54577 (57660) hydrogen bonds : bond 0.04251 ( 1825) hydrogen bonds : angle 4.20431 ( 5262) metal coordination : bond 0.00279 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 353 time to evaluate : 1.153 Fit side-chains REVERT: B 389 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8184 (tm-30) REVERT: B 402 MET cc_start: 0.7767 (mtm) cc_final: 0.7479 (mtt) REVERT: C 389 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8099 (tt0) REVERT: D 285 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8475 (t80) REVERT: E 389 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: E 402 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7479 (mtt) REVERT: F 285 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8383 (t80) REVERT: F 389 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: G 285 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8487 (t80) REVERT: G 292 MET cc_start: 0.6994 (mtp) cc_final: 0.6732 (mtm) REVERT: H 389 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: I 389 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: J 389 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: K 73 MET cc_start: 0.5580 (tpp) cc_final: 0.5342 (tmm) REVERT: L 24 MET cc_start: 0.6160 (pmt) cc_final: 0.5688 (pmt) REVERT: L 285 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8409 (t80) REVERT: L 389 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: L 402 MET cc_start: 0.7792 (mtm) cc_final: 0.7508 (mtt) outliers start: 80 outliers final: 53 residues processed: 425 average time/residue: 0.6640 time to fit residues: 347.6215 Evaluate side-chains 414 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 222 ARG Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 300 optimal weight: 1.9990 chunk 321 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 501 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 247 optimal weight: 0.4980 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 9.9990 chunk 386 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.208011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.167286 restraints weight = 83617.179| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.26 r_work: 0.3233 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 42600 Z= 0.131 Angle : 0.568 10.233 57660 Z= 0.298 Chirality : 0.045 0.189 6552 Planarity : 0.005 0.045 7308 Dihedral : 4.728 59.832 5836 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.01 % Allowed : 17.83 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.11), residues: 5268 helix: 2.26 (0.14), residues: 1680 sheet: 0.69 (0.15), residues: 1152 loop : -1.54 (0.10), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.012 0.001 TYR D 248 PHE 0.016 0.002 PHE C 183 TRP 0.009 0.001 TRP F 421 HIS 0.002 0.001 HIS A 307 Details of bonding type rmsd covalent geometry : bond 0.00272 (42564) covalent geometry : angle 0.56796 (57660) hydrogen bonds : bond 0.04909 ( 1825) hydrogen bonds : angle 4.29290 ( 5262) metal coordination : bond 0.00312 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 345 time to evaluate : 1.536 Fit side-chains REVERT: B 389 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8189 (tm-30) REVERT: B 402 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7639 (mtt) REVERT: C 389 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: D 285 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8471 (t80) REVERT: E 73 MET cc_start: 0.5561 (tpp) cc_final: 0.4946 (tmm) REVERT: E 221 ARG cc_start: 0.6035 (mmt180) cc_final: 0.5745 (mtt-85) REVERT: E 389 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: E 402 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7650 (mtt) REVERT: F 285 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.8414 (t80) REVERT: F 389 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: G 18 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6734 (mp) REVERT: G 285 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8487 (t80) REVERT: G 292 MET cc_start: 0.7000 (mtp) cc_final: 0.6728 (mtm) REVERT: H 389 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: I 389 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: J 389 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7923 (tm-30) REVERT: J 412 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6339 (pp20) REVERT: K 73 MET cc_start: 0.5603 (tpp) cc_final: 0.5360 (tmm) REVERT: L 24 MET cc_start: 0.6170 (pmt) cc_final: 0.5708 (pmt) REVERT: L 285 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8403 (t80) REVERT: L 389 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: L 402 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7647 (mtt) outliers start: 90 outliers final: 56 residues processed: 425 average time/residue: 0.6782 time to fit residues: 356.0342 Evaluate side-chains 412 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 402 MET Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 412 GLU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 402 MET Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 45 optimal weight: 3.9990 chunk 398 optimal weight: 0.7980 chunk 277 optimal weight: 2.9990 chunk 476 optimal weight: 0.9980 chunk 301 optimal weight: 0.7980 chunk 235 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 444 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.207172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.166035 restraints weight = 87446.715| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.35 r_work: 0.3214 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42600 Z= 0.143 Angle : 0.591 13.505 57660 Z= 0.312 Chirality : 0.046 0.144 6552 Planarity : 0.005 0.045 7308 Dihedral : 4.836 59.818 5836 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.87 % Allowed : 17.89 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.11), residues: 5268 helix: 2.19 (0.14), residues: 1680 sheet: 0.64 (0.15), residues: 1152 loop : -1.53 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.013 0.001 TYR D 248 PHE 0.018 0.002 PHE C 183 TRP 0.009 0.002 TRP L 421 HIS 0.003 0.001 HIS G 307 Details of bonding type rmsd covalent geometry : bond 0.00298 (42564) covalent geometry : angle 0.59100 (57660) hydrogen bonds : bond 0.05357 ( 1825) hydrogen bonds : angle 4.38379 ( 5262) metal coordination : bond 0.00304 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10536 Ramachandran restraints generated. 5268 Oldfield, 0 Emsley, 5268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 343 time to evaluate : 1.456 Fit side-chains REVERT: B 389 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: C 389 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: D 285 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8504 (t80) REVERT: E 73 MET cc_start: 0.5614 (tpp) cc_final: 0.5124 (tmt) REVERT: E 221 ARG cc_start: 0.6055 (mmt180) cc_final: 0.5758 (mtt-85) REVERT: E 389 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: F 285 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8430 (t80) REVERT: F 389 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: G 18 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6721 (mp) REVERT: G 285 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.8523 (t80) REVERT: G 292 MET cc_start: 0.7047 (mtp) cc_final: 0.6786 (mtm) REVERT: H 389 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: I 389 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: J 389 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: J 412 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6367 (pp20) REVERT: L 24 MET cc_start: 0.6234 (pmt) cc_final: 0.5775 (pmt) REVERT: L 285 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8433 (t80) REVERT: L 389 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8220 (tm-30) outliers start: 84 outliers final: 59 residues processed: 417 average time/residue: 0.6557 time to fit residues: 339.2509 Evaluate side-chains 412 residues out of total 4596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 339 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 214 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 320 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 214 SER Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 202 GLU Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 320 THR Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 202 GLU Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 222 ARG Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 320 THR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain H residue 472 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain J residue 214 SER Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 389 GLN Chi-restraints excluded: chain J residue 412 GLU Chi-restraints excluded: chain J residue 472 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 202 GLU Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 320 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain L residue 139 VAL Chi-restraints excluded: chain L residue 202 GLU Chi-restraints excluded: chain L residue 214 SER Chi-restraints excluded: chain L residue 280 VAL Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 389 GLN Chi-restraints excluded: chain L residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 44 optimal weight: 10.0000 chunk 453 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 408 optimal weight: 9.9990 chunk 493 optimal weight: 0.9980 chunk 478 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 520 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.206587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.154496 restraints weight = 96232.680| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 5.56 r_work: 0.3120 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42600 Z= 0.154 Angle : 0.610 9.958 57660 Z= 0.324 Chirality : 0.046 0.163 6552 Planarity : 0.005 0.045 7308 Dihedral : 4.933 59.818 5836 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.65 % Allowed : 18.27 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.11), residues: 5268 helix: 2.09 (0.14), residues: 1680 sheet: 0.58 (0.15), residues: 1152 loop : -1.56 (0.11), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 110 TYR 0.014 0.002 TYR D 248 PHE 0.020 0.002 PHE F 183 TRP 0.010 0.002 TRP J 175 HIS 0.003 0.001 HIS K 307 Details of bonding type rmsd covalent geometry : bond 0.00322 (42564) covalent geometry : angle 0.61034 (57660) hydrogen bonds : bond 0.05688 ( 1825) hydrogen bonds : angle 4.44839 ( 5262) metal coordination : bond 0.00339 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16024.23 seconds wall clock time: 273 minutes 10.47 seconds (16390.47 seconds total)