Starting phenix.real_space_refine on Fri Feb 6 01:38:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.map" model { file = "/net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uio_64199/02_2026/9uio_64199.cif" } resolution = 3.03 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= 0.195 sd= 0.995 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 165 5.16 5 C 13620 2.51 5 N 3717 2.21 5 O 4083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21591 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "B" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain: "R" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "C" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "D" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain: "S" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "E" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3326 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 411} Chain: "F" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3268 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 27, 'TRANS': 390} Chain: "T" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 601 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.76, per 1000 atoms: 0.22 Number of scatterers: 21591 At special positions: 0 Unit cell: (162.47, 152.975, 177.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 165 16.00 O 4083 8.00 N 3717 7.00 C 13620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.02 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.04 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 25 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS R 33 " - pdb=" SG CYS R 45 " distance=2.03 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 58 " distance=2.03 Simple disulfide: pdb=" SG CYS R 52 " - pdb=" SG CYS R 67 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 84 " distance=2.03 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.03 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 16 " - pdb=" SG CYS D 124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 25 " distance=2.03 Simple disulfide: pdb=" SG CYS D 91 " - pdb=" SG CYS D 105 " distance=2.03 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 266 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 220 " distance=2.03 Simple disulfide: pdb=" SG CYS S 33 " - pdb=" SG CYS S 45 " distance=2.03 Simple disulfide: pdb=" SG CYS S 40 " - pdb=" SG CYS S 58 " distance=2.03 Simple disulfide: pdb=" SG CYS S 52 " - pdb=" SG CYS S 67 " distance=2.03 Simple disulfide: pdb=" SG CYS S 72 " - pdb=" SG CYS S 84 " distance=2.03 Simple disulfide: pdb=" SG CYS S 79 " - pdb=" SG CYS S 97 " distance=2.04 Simple disulfide: pdb=" SG CYS S 91 " - pdb=" SG CYS S 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.03 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.03 Simple disulfide: pdb=" SG CYS F 16 " - pdb=" SG CYS F 124 " distance=2.03 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 25 " distance=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.03 Simple disulfide: pdb=" SG CYS F 152 " - pdb=" SG CYS F 266 " distance=2.03 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 226 " distance=2.03 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS T 33 " - pdb=" SG CYS T 45 " distance=2.04 Simple disulfide: pdb=" SG CYS T 40 " - pdb=" SG CYS T 58 " distance=2.03 Simple disulfide: pdb=" SG CYS T 52 " - pdb=" SG CYS T 67 " distance=2.03 Simple disulfide: pdb=" SG CYS T 72 " - pdb=" SG CYS T 84 " distance=2.03 Simple disulfide: pdb=" SG CYS T 79 " - pdb=" SG CYS T 97 " distance=2.03 Simple disulfide: pdb=" SG CYS T 91 " - pdb=" SG CYS T 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5232 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 53 sheets defined 14.1% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.082A pdb=" N THR A 115 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 403 through 439 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.505A pdb=" N LEU B 8 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 363 through 398 removed outlier: 4.315A pdb=" N GLY B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.054A pdb=" N THR C 115 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 246 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 403 through 439 removed outlier: 3.583A pdb=" N ILE C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'D' and resid 222 through 224 No H-bonds generated for 'chain 'D' and resid 222 through 224' Processing helix chain 'D' and resid 351 through 363 Processing helix chain 'D' and resid 363 through 398 removed outlier: 4.161A pdb=" N GLY D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N SER D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'S' and resid 49 through 51 No H-bonds generated for 'chain 'S' and resid 49 through 51' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 100 through 104 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.830A pdb=" N THR E 115 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 403 through 439 removed outlier: 3.808A pdb=" N MET E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU E 434 " --> pdb=" O CYS E 430 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG E 439 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 180 Processing helix chain 'F' and resid 222 through 224 No H-bonds generated for 'chain 'F' and resid 222 through 224' Processing helix chain 'F' and resid 351 through 363 Processing helix chain 'F' and resid 363 through 383 removed outlier: 4.163A pdb=" N GLY F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 398 Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'T' and resid 49 through 51 No H-bonds generated for 'chain 'T' and resid 49 through 51' Processing helix chain 'T' and resid 88 through 90 No H-bonds generated for 'chain 'T' and resid 88 through 90' Processing helix chain 'T' and resid 100 through 104 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 27 through 31 current: chain 'A' and resid 119 through 137 removed outlier: 4.586A pdb=" N LEU A 129 " --> pdb=" O VAL A 148 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 140 through 148 current: chain 'A' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 185 current: chain 'A' and resid 267 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 101 through 110 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 302 removed outlier: 3.844A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 352 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.540A pdb=" N GLY A 326 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 387 through 388 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 387 through 388 current: chain 'B' and resid 282 through 299 removed outlier: 7.556A pdb=" N LEU B 285 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N PHE B 319 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU B 287 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ARG B 317 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ALA B 289 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR B 315 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ARG B 291 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLY B 313 " --> pdb=" O ARG B 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 307 through 320 current: chain 'B' and resid 336 through 340 Processing sheet with id=AB1, first strand: chain 'B' and resid 2 through 3 removed outlier: 4.453A pdb=" N HIS B 256 " --> pdb=" O THR B 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB3, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.617A pdb=" N GLN B 46 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 34 " --> pdb=" O ARG B 44 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 10.153A pdb=" N SER B 48 " --> pdb=" O MET B 67 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET B 67 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS B 63 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.540A pdb=" N SER B 110 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N LYS B 128 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N THR B 112 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL B 126 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER B 114 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N CYS B 124 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 148 through 155 Processing sheet with id=AB6, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AB7, first strand: chain 'R' and resid 37 through 39 Processing sheet with id=AB8, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AB9, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.716A pdb=" N VAL C 161 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 14 through 21 removed outlier: 5.154A pdb=" N ARG C 21 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL C 34 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU C 133 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 36 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 131 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 38 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU C 129 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA C 127 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 42 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS C 125 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS C 44 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS C 123 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 46 " --> pdb=" O ALA C 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 119 through 133 current: chain 'C' and resid 140 through 141 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 140 through 141 current: chain 'C' and resid 183 through 186 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 183 through 186 current: chain 'C' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 101 through 110 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC4, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AC5, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AC6, first strand: chain 'C' and resid 300 through 303 removed outlier: 3.540A pdb=" N GLY C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 343 through 346 removed outlier: 3.769A pdb=" N GLY C 326 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 387 through 388 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 387 through 388 current: chain 'D' and resid 282 through 299 removed outlier: 7.559A pdb=" N LEU D 285 " --> pdb=" O PHE D 319 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N PHE D 319 " --> pdb=" O LEU D 285 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU D 287 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ARG D 317 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA D 289 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR D 315 " --> pdb=" O ALA D 289 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ARG D 291 " --> pdb=" O GLY D 313 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N GLY D 313 " --> pdb=" O ARG D 291 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 319 current: chain 'D' and resid 336 through 340 Processing sheet with id=AC9, first strand: chain 'D' and resid 2 through 3 removed outlier: 4.427A pdb=" N HIS D 256 " --> pdb=" O THR D 3 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AD2, first strand: chain 'D' and resid 31 through 35 removed outlier: 6.635A pdb=" N GLN D 46 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL D 34 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG D 44 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 16.607A pdb=" N GLN D 46 " --> pdb=" O TYR D 66 " (cutoff:3.500A) removed outlier: 13.375A pdb=" N TYR D 66 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 11.552A pdb=" N SER D 48 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N PHE D 64 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N GLN D 50 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 9.380A pdb=" N THR D 62 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY D 52 " --> pdb=" O ASP D 60 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.107A pdb=" N ASP D 109 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AD5, first strand: chain 'D' and resid 206 through 211 removed outlier: 3.571A pdb=" N GLY D 209 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 37 through 39 Processing sheet with id=AD7, first strand: chain 'S' and resid 76 through 78 Processing sheet with id=AD8, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.510A pdb=" N ILE E 280 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AE1, first strand: chain 'E' and resid 33 through 48 removed outlier: 6.716A pdb=" N VAL E 33 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU E 133 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N SER E 35 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N VAL E 131 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU E 37 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU E 129 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR E 39 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA E 127 " --> pdb=" O THR E 39 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER E 41 " --> pdb=" O HIS E 125 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA E 121 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL E 47 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA E 119 " --> pdb=" O VAL E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 144 through 147 current: chain 'E' and resid 183 through 185 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 183 through 185 current: chain 'E' and resid 267 through 269 Processing sheet with id=AE2, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 101 through 110 No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AE4, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AE5, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AE6, first strand: chain 'E' and resid 296 through 306 removed outlier: 3.796A pdb=" N GLU E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N SER E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AE8, first strand: chain 'E' and resid 387 through 388 removed outlier: 3.511A pdb=" N THR F 297 " --> pdb=" O THR F 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AF1, first strand: chain 'F' and resid 31 through 35 removed outlier: 8.770A pdb=" N ILE F 31 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N SER F 48 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN F 33 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 16.495A pdb=" N GLN F 46 " --> pdb=" O TYR F 66 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N TYR F 66 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 11.510A pdb=" N SER F 48 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N PHE F 64 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 11.282A pdb=" N GLN F 50 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N THR F 62 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY F 52 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 83 through 86 removed outlier: 4.214A pdb=" N ASP F 109 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 148 through 155 Processing sheet with id=AF4, first strand: chain 'F' and resid 237 through 238 Processing sheet with id=AF5, first strand: chain 'F' and resid 206 through 211 Processing sheet with id=AF6, first strand: chain 'F' and resid 275 through 279 removed outlier: 3.625A pdb=" N GLY F 282 " --> pdb=" O TRP F 279 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'T' and resid 37 through 39 Processing sheet with id=AF8, first strand: chain 'T' and resid 76 through 78 577 hydrogen bonds defined for protein. 1521 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: 3.24 Time building geometry restraints manager: 2.33 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: 7029 1.34 - 1.46: 5180 1.46 - 1.58: 9739 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 22140 Sorted by residual: bond pdb=" C THR D 398 " pdb=" N PRO D 399 " ideal model delta sigma weight residual 1.335 1.366 -0.030 1.36e-02 5.41e+03 4.99e+00 bond pdb=" C THR F 398 " pdb=" N PRO F 399 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.30e-02 5.92e+03 2.33e+00 bond pdb=" CB CYS R 52 " pdb=" SG CYS R 52 " ideal model delta sigma weight residual 1.808 1.763 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" CA ASN T 81 " pdb=" CB ASN T 81 " ideal model delta sigma weight residual 1.528 1.548 -0.020 1.56e-02 4.11e+03 1.57e+00 bond pdb=" C THR B 398 " pdb=" N PRO B 399 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 ... (remaining 22135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 29946 3.02 - 6.04: 175 6.04 - 9.06: 16 9.06 - 12.08: 8 12.08 - 15.10: 2 Bond angle restraints: 30147 Sorted by residual: angle pdb=" N SER D 88 " pdb=" CA SER D 88 " pdb=" C SER D 88 " ideal model delta sigma weight residual 113.43 107.53 5.90 1.26e+00 6.30e-01 2.19e+01 angle pdb=" CA LEU E 428 " pdb=" CB LEU E 428 " pdb=" CG LEU E 428 " ideal model delta sigma weight residual 116.30 131.40 -15.10 3.50e+00 8.16e-02 1.86e+01 angle pdb=" CB ARG F 393 " pdb=" CG ARG F 393 " pdb=" CD ARG F 393 " ideal model delta sigma weight residual 111.30 120.60 -9.30 2.30e+00 1.89e-01 1.64e+01 angle pdb=" CB MET A 433 " pdb=" CG MET A 433 " pdb=" SD MET A 433 " ideal model delta sigma weight residual 112.70 124.01 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA LEU F 379 " pdb=" CB LEU F 379 " pdb=" CG LEU F 379 " ideal model delta sigma weight residual 116.30 129.16 -12.86 3.50e+00 8.16e-02 1.35e+01 ... (remaining 30142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11336 17.97 - 35.93: 1543 35.93 - 53.90: 407 53.90 - 71.86: 67 71.86 - 89.83: 21 Dihedral angle restraints: 13374 sinusoidal: 5235 harmonic: 8139 Sorted by residual: dihedral pdb=" CB CYS T 33 " pdb=" SG CYS T 33 " pdb=" SG CYS T 45 " pdb=" CB CYS T 45 " ideal model delta sinusoidal sigma weight residual 93.00 176.42 -83.42 1 1.00e+01 1.00e-02 8.50e+01 dihedral pdb=" CB CYS S 72 " pdb=" SG CYS S 72 " pdb=" SG CYS S 84 " pdb=" CB CYS S 84 " ideal model delta sinusoidal sigma weight residual 93.00 175.29 -82.29 1 1.00e+01 1.00e-02 8.31e+01 dihedral pdb=" CB CYS R 33 " pdb=" SG CYS R 33 " pdb=" SG CYS R 45 " pdb=" CB CYS R 45 " ideal model delta sinusoidal sigma weight residual -86.00 -158.41 72.41 1 1.00e+01 1.00e-02 6.70e+01 ... (remaining 13371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2841 0.060 - 0.119: 508 0.119 - 0.179: 40 0.179 - 0.239: 3 0.239 - 0.299: 1 Chirality restraints: 3393 Sorted by residual: chirality pdb=" CG LEU E 420 " pdb=" CB LEU E 420 " pdb=" CD1 LEU E 420 " pdb=" CD2 LEU E 420 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL F 414 " pdb=" CA VAL F 414 " pdb=" CG1 VAL F 414 " pdb=" CG2 VAL F 414 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CA MET A 433 " pdb=" N MET A 433 " pdb=" C MET A 433 " pdb=" CB MET A 433 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.55e-01 ... (remaining 3390 not shown) Planarity restraints: 3873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 152 " 0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A 153 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 381 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.67e+00 pdb=" C GLY D 381 " 0.048 2.00e-02 2.50e+03 pdb=" O GLY D 381 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 382 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 381 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C GLY B 381 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY B 381 " 0.017 2.00e-02 2.50e+03 pdb=" N THR B 382 " 0.016 2.00e-02 2.50e+03 ... (remaining 3870 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 515 2.70 - 3.25: 20374 3.25 - 3.80: 33870 3.80 - 4.35: 44153 4.35 - 4.90: 74326 Nonbonded interactions: 173238 Sorted by model distance: nonbonded pdb=" O ASP S 55 " pdb="CA CA S 202 " model vdw 2.152 2.510 nonbonded pdb=" O TRP S 50 " pdb="CA CA S 202 " model vdw 2.167 2.510 nonbonded pdb=" O ASP T 55 " pdb="CA CA T 202 " model vdw 2.168 2.510 nonbonded pdb=" OD2 ASP S 96 " pdb="CA CA S 201 " model vdw 2.199 2.510 nonbonded pdb=" O TRP R 50 " pdb="CA CA R 202 " model vdw 2.202 2.510 ... (remaining 173233 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 19.190 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22197 Z= 0.153 Angle : 0.684 15.105 30261 Z= 0.356 Chirality : 0.045 0.299 3393 Planarity : 0.005 0.091 3873 Dihedral : 17.178 89.830 7971 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 30.58 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.48 (0.16), residues: 2790 helix: 0.83 (0.29), residues: 288 sheet: -0.06 (0.17), residues: 936 loop : -0.65 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 394 TYR 0.043 0.001 TYR E 308 PHE 0.025 0.001 PHE T 38 TRP 0.040 0.002 TRP E 409 HIS 0.004 0.001 HIS D 353 Details of bonding type rmsd covalent geometry : bond 0.00330 (22140) covalent geometry : angle 0.68044 (30147) SS BOND : bond 0.00292 ( 57) SS BOND : angle 1.28010 ( 114) hydrogen bonds : bond 0.17467 ( 577) hydrogen bonds : angle 7.44046 ( 1521) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9072 (mmmt) cc_final: 0.8863 (mmmt) REVERT: A 320 TYR cc_start: 0.8540 (p90) cc_final: 0.7933 (p90) REVERT: B 396 CYS cc_start: 0.8473 (t) cc_final: 0.8227 (p) REVERT: C 21 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6086 (mtp-110) REVERT: D 81 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8957 (mt-10) REVERT: D 366 TYR cc_start: 0.8860 (m-80) cc_final: 0.8654 (m-80) REVERT: D 393 ARG cc_start: 0.9363 (mmm-85) cc_final: 0.8999 (tpp80) REVERT: S 57 ASP cc_start: 0.8852 (t0) cc_final: 0.8475 (t0) REVERT: E 30 GLU cc_start: 0.8177 (tt0) cc_final: 0.7925 (tm-30) REVERT: E 195 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8972 (ptp) REVERT: E 303 VAL cc_start: 0.9457 (OUTLIER) cc_final: 0.9250 (m) REVERT: E 407 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (m100) REVERT: E 419 SER cc_start: 0.9505 (t) cc_final: 0.9252 (p) REVERT: F 303 ARG cc_start: 0.9216 (ttp80) cc_final: 0.8965 (ttp80) REVERT: F 393 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8422 (tpt170) outliers start: 58 outliers final: 37 residues processed: 321 average time/residue: 0.1673 time to fit residues: 80.5974 Evaluate side-chains 293 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain S residue 33 CYS Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 372 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 59 GLN A 100 ASN A 327 HIS A 345 HIS A 436 ASN ** B 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 HIS B 169 HIS ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 249 HIS B 252 GLN B 332 ASN B 341 GLN C 59 GLN C 100 ASN C 228 ASN ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN D 153 HIS D 196 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 252 GLN D 318 ASN D 332 ASN D 353 HIS S 39 GLN E 43 ASN E 59 GLN E 100 ASN E 345 HIS E 396 GLN F 196 ASN F 249 HIS F 252 GLN F 318 ASN F 332 ASN T 39 GLN ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.056471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.041219 restraints weight = 62500.309| |-----------------------------------------------------------------------------| r_work (start): 0.2455 rms_B_bonded: 2.23 r_work: 0.2363 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2262 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22197 Z= 0.195 Angle : 0.614 10.738 30261 Z= 0.315 Chirality : 0.045 0.201 3393 Planarity : 0.005 0.057 3873 Dihedral : 6.158 59.540 3091 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.13 % Allowed : 26.12 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.16), residues: 2790 helix: 0.71 (0.29), residues: 306 sheet: 0.09 (0.17), residues: 957 loop : -0.61 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 231 TYR 0.020 0.002 TYR A 308 PHE 0.019 0.002 PHE R 77 TRP 0.024 0.002 TRP T 89 HIS 0.005 0.001 HIS D 353 Details of bonding type rmsd covalent geometry : bond 0.00454 (22140) covalent geometry : angle 0.61195 (30147) SS BOND : bond 0.00333 ( 57) SS BOND : angle 1.03453 ( 114) hydrogen bonds : bond 0.04103 ( 577) hydrogen bonds : angle 5.75140 ( 1521) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 253 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8958 (mmmt) REVERT: A 320 TYR cc_start: 0.8544 (p90) cc_final: 0.7779 (p90) REVERT: B 235 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.8615 (mttm) REVERT: B 393 ARG cc_start: 0.8947 (tpt170) cc_final: 0.8641 (tpt170) REVERT: B 396 CYS cc_start: 0.8693 (t) cc_final: 0.8387 (p) REVERT: R 37 GLN cc_start: 0.9009 (mt0) cc_final: 0.8688 (mt0) REVERT: R 44 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8108 (tmm-80) REVERT: D 218 ASN cc_start: 0.8874 (m-40) cc_final: 0.8671 (m110) REVERT: D 393 ARG cc_start: 0.9390 (mmm-85) cc_final: 0.9076 (tpp80) REVERT: S 57 ASP cc_start: 0.9102 (t0) cc_final: 0.8691 (t0) REVERT: S 76 ASP cc_start: 0.7744 (t70) cc_final: 0.7523 (t70) REVERT: E 160 LYS cc_start: 0.8921 (mtmm) cc_final: 0.8654 (mtmm) REVERT: E 195 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.8967 (ptp) REVERT: E 212 ASP cc_start: 0.9024 (p0) cc_final: 0.8738 (p0) REVERT: E 303 VAL cc_start: 0.9539 (OUTLIER) cc_final: 0.9306 (m) REVERT: E 320 TYR cc_start: 0.8416 (p90) cc_final: 0.8074 (p90) REVERT: E 419 SER cc_start: 0.9510 (t) cc_final: 0.9255 (p) REVERT: F 394 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.8892 (mmm-85) outliers start: 123 outliers final: 70 residues processed: 355 average time/residue: 0.1470 time to fit residues: 79.8054 Evaluate side-chains 316 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 242 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain S residue 34 GLU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 214 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 149 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 HIS F 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.057086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.041844 restraints weight = 62214.805| |-----------------------------------------------------------------------------| r_work (start): 0.2478 rms_B_bonded: 2.24 r_work: 0.2386 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2285 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9083 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 22197 Z= 0.139 Angle : 0.576 11.369 30261 Z= 0.293 Chirality : 0.044 0.172 3393 Planarity : 0.004 0.048 3873 Dihedral : 5.543 57.136 3064 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.80 % Allowed : 26.24 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.25 (0.16), residues: 2790 helix: 0.79 (0.29), residues: 306 sheet: 0.20 (0.17), residues: 942 loop : -0.54 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 303 TYR 0.019 0.001 TYR F 328 PHE 0.020 0.001 PHE R 77 TRP 0.018 0.001 TRP E 409 HIS 0.004 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00324 (22140) covalent geometry : angle 0.57309 (30147) SS BOND : bond 0.00292 ( 57) SS BOND : angle 1.05695 ( 114) hydrogen bonds : bond 0.03639 ( 577) hydrogen bonds : angle 5.48017 ( 1521) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 258 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9202 (mmmt) cc_final: 0.8998 (mmmt) REVERT: A 298 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 320 TYR cc_start: 0.8605 (p90) cc_final: 0.7804 (p90) REVERT: A 327 HIS cc_start: 0.8309 (OUTLIER) cc_final: 0.7893 (m-70) REVERT: B 393 ARG cc_start: 0.8954 (tpt170) cc_final: 0.8633 (tpt170) REVERT: B 396 CYS cc_start: 0.8708 (t) cc_final: 0.8394 (p) REVERT: R 37 GLN cc_start: 0.9074 (mt0) cc_final: 0.8716 (mt0) REVERT: R 44 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8159 (tmm-80) REVERT: C 21 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7786 (mtp85) REVERT: D 81 GLU cc_start: 0.9433 (OUTLIER) cc_final: 0.9130 (mt-10) REVERT: D 218 ASN cc_start: 0.8878 (m-40) cc_final: 0.8667 (m110) REVERT: D 354 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8469 (mt-10) REVERT: D 393 ARG cc_start: 0.9387 (mmm-85) cc_final: 0.8981 (tpp80) REVERT: S 57 ASP cc_start: 0.9085 (t0) cc_final: 0.8677 (t0) REVERT: E 160 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8728 (mtmm) REVERT: E 195 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.8839 (ptp) REVERT: E 212 ASP cc_start: 0.9026 (p0) cc_final: 0.8728 (p0) REVERT: E 303 VAL cc_start: 0.9507 (OUTLIER) cc_final: 0.9301 (m) REVERT: E 320 TYR cc_start: 0.8377 (p90) cc_final: 0.8108 (p90) REVERT: E 419 SER cc_start: 0.9523 (t) cc_final: 0.9264 (p) REVERT: F 394 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.8949 (mmm-85) REVERT: T 37 GLN cc_start: 0.9073 (mt0) cc_final: 0.8822 (mt0) outliers start: 115 outliers final: 76 residues processed: 354 average time/residue: 0.1516 time to fit residues: 82.4025 Evaluate side-chains 329 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 77 PHE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain E residue 407 TRP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 178 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 260 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 192 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 345 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 HIS C 100 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS ** E 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.041462 restraints weight = 62640.991| |-----------------------------------------------------------------------------| r_work (start): 0.2466 rms_B_bonded: 2.20 r_work: 0.2375 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 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 : 0.004 0.042 22197 Z= 0.179 Angle : 0.604 12.215 30261 Z= 0.306 Chirality : 0.044 0.161 3393 Planarity : 0.005 0.063 3873 Dihedral : 5.483 57.100 3057 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.34 % Allowed : 25.82 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.19 (0.16), residues: 2790 helix: 0.87 (0.29), residues: 309 sheet: 0.24 (0.17), residues: 942 loop : -0.52 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 303 TYR 0.018 0.001 TYR F 328 PHE 0.022 0.002 PHE R 77 TRP 0.020 0.001 TRP E 409 HIS 0.005 0.001 HIS F 349 Details of bonding type rmsd covalent geometry : bond 0.00420 (22140) covalent geometry : angle 0.60036 (30147) SS BOND : bond 0.00340 ( 57) SS BOND : angle 1.18064 ( 114) hydrogen bonds : bond 0.03651 ( 577) hydrogen bonds : angle 5.36716 ( 1521) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 255 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7742 (tm-30) REVERT: A 327 HIS cc_start: 0.8181 (OUTLIER) cc_final: 0.7626 (m-70) REVERT: A 339 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 2 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8940 (mt) REVERT: B 235 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8542 (mttm) REVERT: B 393 ARG cc_start: 0.9030 (tpt170) cc_final: 0.8689 (tpt170) REVERT: B 396 CYS cc_start: 0.8734 (t) cc_final: 0.8403 (p) REVERT: R 37 GLN cc_start: 0.9012 (mt0) cc_final: 0.8622 (mt0) REVERT: R 44 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8062 (tmm-80) REVERT: C 21 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7777 (mtp85) REVERT: D 81 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9099 (mt-10) REVERT: D 231 ARG cc_start: 0.9194 (mtp85) cc_final: 0.8934 (mtt90) REVERT: D 354 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: D 393 ARG cc_start: 0.9395 (mmm-85) cc_final: 0.8984 (tpp80) REVERT: S 57 ASP cc_start: 0.9085 (t0) cc_final: 0.8674 (t0) REVERT: S 97 CYS cc_start: 0.5608 (t) cc_final: 0.5399 (t) REVERT: E 24 TYR cc_start: 0.8542 (m-80) cc_final: 0.7498 (m-80) REVERT: E 212 ASP cc_start: 0.9006 (p0) cc_final: 0.8713 (p0) REVERT: E 320 TYR cc_start: 0.8384 (p90) cc_final: 0.8104 (p90) REVERT: E 419 SER cc_start: 0.9534 (t) cc_final: 0.9285 (p) REVERT: F 393 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8656 (mmm160) REVERT: F 394 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.9030 (tpp80) outliers start: 128 outliers final: 93 residues processed: 363 average time/residue: 0.1505 time to fit residues: 83.9609 Evaluate side-chains 348 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 248 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 189 optimal weight: 0.5980 chunk 246 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 214 optimal weight: 5.9990 chunk 212 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 362 GLN D 55 GLN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 249 HIS E 100 ASN E 345 HIS F 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.056448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.041536 restraints weight = 62463.005| |-----------------------------------------------------------------------------| r_work (start): 0.2464 rms_B_bonded: 2.20 r_work: 0.2373 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2272 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9104 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22197 Z= 0.179 Angle : 0.604 12.436 30261 Z= 0.306 Chirality : 0.044 0.161 3393 Planarity : 0.005 0.064 3873 Dihedral : 5.433 51.929 3056 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.63 % Allowed : 25.49 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.14 (0.16), residues: 2790 helix: 0.85 (0.29), residues: 309 sheet: 0.29 (0.17), residues: 939 loop : -0.48 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 289 TYR 0.018 0.001 TYR F 328 PHE 0.021 0.002 PHE R 77 TRP 0.016 0.001 TRP E 409 HIS 0.017 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00421 (22140) covalent geometry : angle 0.60279 (30147) SS BOND : bond 0.00346 ( 57) SS BOND : angle 0.93485 ( 114) hydrogen bonds : bond 0.03573 ( 577) hydrogen bonds : angle 5.32328 ( 1521) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 254 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8792 (mmmt) REVERT: A 298 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 339 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8778 (mp) REVERT: B 2 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8926 (mt) REVERT: B 235 LYS cc_start: 0.9468 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: B 393 ARG cc_start: 0.9063 (tpt170) cc_final: 0.8707 (tpt170) REVERT: B 396 CYS cc_start: 0.8666 (t) cc_final: 0.8356 (p) REVERT: R 37 GLN cc_start: 0.9003 (mt0) cc_final: 0.8602 (mt0) REVERT: R 44 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8125 (tmm-80) REVERT: C 21 ARG cc_start: 0.8219 (mtp-110) cc_final: 0.7764 (mtp85) REVERT: C 414 PHE cc_start: 0.8831 (m-10) cc_final: 0.8586 (m-10) REVERT: D 81 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9110 (mt-10) REVERT: D 231 ARG cc_start: 0.9174 (mtp85) cc_final: 0.8944 (mtt90) REVERT: D 354 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: D 393 ARG cc_start: 0.9408 (mmm-85) cc_final: 0.8996 (tpp80) REVERT: S 57 ASP cc_start: 0.9082 (t0) cc_final: 0.8689 (t0) REVERT: E 24 TYR cc_start: 0.8493 (m-80) cc_final: 0.8215 (m-80) REVERT: E 30 GLU cc_start: 0.8424 (tp30) cc_final: 0.8094 (tp30) REVERT: E 212 ASP cc_start: 0.9011 (p0) cc_final: 0.8719 (p0) REVERT: E 320 TYR cc_start: 0.8372 (p90) cc_final: 0.8129 (p90) REVERT: E 364 ASN cc_start: 0.8970 (t0) cc_final: 0.8678 (t0) REVERT: E 373 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8703 (mmtp) REVERT: E 419 SER cc_start: 0.9534 (t) cc_final: 0.9284 (p) REVERT: F 30 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.9015 (tttp) REVERT: F 394 ARG cc_start: 0.9280 (mmm-85) cc_final: 0.9048 (tpp80) outliers start: 135 outliers final: 103 residues processed: 367 average time/residue: 0.1597 time to fit residues: 90.2928 Evaluate side-chains 359 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 249 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 105 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 116 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 266 optimal weight: 2.9990 chunk 225 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 190 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 362 GLN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS E 362 GLN F 21 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.054512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.039710 restraints weight = 62964.871| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 2.20 r_work: 0.2325 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2223 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 22197 Z= 0.297 Angle : 0.680 12.694 30261 Z= 0.347 Chirality : 0.047 0.190 3393 Planarity : 0.005 0.066 3873 Dihedral : 5.698 50.083 3055 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 6.17 % Allowed : 25.32 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.23 (0.16), residues: 2790 helix: 1.10 (0.30), residues: 291 sheet: 0.23 (0.17), residues: 954 loop : -0.61 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 289 TYR 0.023 0.002 TYR E 308 PHE 0.027 0.002 PHE R 77 TRP 0.024 0.002 TRP E 409 HIS 0.024 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00697 (22140) covalent geometry : angle 0.67777 (30147) SS BOND : bond 0.00509 ( 57) SS BOND : angle 1.06111 ( 114) hydrogen bonds : bond 0.04076 ( 577) hydrogen bonds : angle 5.47463 ( 1521) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 254 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8848 (mm-30) REVERT: A 160 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8902 (mmmt) REVERT: A 298 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 339 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8846 (mp) REVERT: B 2 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 235 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.8628 (mttm) REVERT: B 393 ARG cc_start: 0.9097 (tpt170) cc_final: 0.8735 (tpt170) REVERT: B 396 CYS cc_start: 0.8681 (t) cc_final: 0.8383 (p) REVERT: B 397 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7869 (tm) REVERT: R 37 GLN cc_start: 0.8963 (mt0) cc_final: 0.8533 (mt0) REVERT: R 44 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: C 21 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7131 (mtp-110) REVERT: C 158 ASP cc_start: 0.8885 (t0) cc_final: 0.8680 (t0) REVERT: D 81 GLU cc_start: 0.9456 (OUTLIER) cc_final: 0.9131 (mt-10) REVERT: D 231 ARG cc_start: 0.9190 (mtp85) cc_final: 0.8925 (mtt90) REVERT: D 354 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: D 393 ARG cc_start: 0.9465 (mmm-85) cc_final: 0.9073 (tpp80) REVERT: S 57 ASP cc_start: 0.9161 (t0) cc_final: 0.8820 (t0) REVERT: E 24 TYR cc_start: 0.8570 (m-80) cc_final: 0.8055 (m-80) REVERT: E 30 GLU cc_start: 0.8504 (tp30) cc_final: 0.8185 (tp30) REVERT: E 44 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9085 (tttt) REVERT: E 212 ASP cc_start: 0.9042 (p0) cc_final: 0.8755 (p0) REVERT: E 364 ASN cc_start: 0.9068 (t0) cc_final: 0.8821 (t0) REVERT: E 373 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8813 (mmtp) REVERT: E 419 SER cc_start: 0.9545 (t) cc_final: 0.9305 (p) REVERT: F 351 TRP cc_start: 0.8315 (OUTLIER) cc_final: 0.7045 (m-90) REVERT: F 394 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.9061 (mmm-85) REVERT: F 398 THR cc_start: 0.9003 (p) cc_final: 0.8586 (p) outliers start: 148 outliers final: 109 residues processed: 377 average time/residue: 0.1572 time to fit residues: 91.0249 Evaluate side-chains 367 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 248 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain E residue 44 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 351 TRP Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 246 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 212 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS A 345 HIS C 100 ASN ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS E 362 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.039920 restraints weight = 62429.708| |-----------------------------------------------------------------------------| r_work (start): 0.2421 rms_B_bonded: 2.18 r_work: 0.2328 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2227 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9126 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22197 Z= 0.254 Angle : 0.658 13.086 30261 Z= 0.335 Chirality : 0.046 0.212 3393 Planarity : 0.005 0.070 3873 Dihedral : 5.668 50.197 3055 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 6.09 % Allowed : 25.16 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.30 (0.16), residues: 2790 helix: 1.05 (0.30), residues: 291 sheet: 0.21 (0.17), residues: 927 loop : -0.67 (0.15), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.020 0.002 TYR F 328 PHE 0.025 0.002 PHE R 77 TRP 0.023 0.002 TRP E 409 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00596 (22140) covalent geometry : angle 0.65672 (30147) SS BOND : bond 0.00436 ( 57) SS BOND : angle 0.99305 ( 114) hydrogen bonds : bond 0.03918 ( 577) hydrogen bonds : angle 5.45579 ( 1521) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 256 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 339 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8827 (mp) REVERT: B 2 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8886 (mt) REVERT: B 235 LYS cc_start: 0.9492 (OUTLIER) cc_final: 0.8606 (mttm) REVERT: B 354 GLU cc_start: 0.8931 (mp0) cc_final: 0.8314 (mp0) REVERT: B 393 ARG cc_start: 0.9118 (tpt170) cc_final: 0.8739 (tpt170) REVERT: B 396 CYS cc_start: 0.8741 (t) cc_final: 0.8440 (p) REVERT: B 397 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7891 (tm) REVERT: R 34 GLU cc_start: 0.8696 (pm20) cc_final: 0.8477 (pm20) REVERT: R 37 GLN cc_start: 0.9019 (mt0) cc_final: 0.8483 (mt0) REVERT: R 44 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8130 (tmm-80) REVERT: C 21 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7778 (mtp85) REVERT: C 158 ASP cc_start: 0.8887 (t0) cc_final: 0.8660 (t0) REVERT: D 81 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9126 (mt-10) REVERT: D 231 ARG cc_start: 0.9171 (mtp85) cc_final: 0.8913 (mtt90) REVERT: D 354 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8530 (mt-10) REVERT: D 393 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9063 (tpp80) REVERT: S 57 ASP cc_start: 0.9161 (t0) cc_final: 0.8927 (t0) REVERT: S 98 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8742 (pm20) REVERT: E 24 TYR cc_start: 0.8559 (m-80) cc_final: 0.8250 (m-80) REVERT: E 30 GLU cc_start: 0.8460 (tp30) cc_final: 0.8171 (tp30) REVERT: E 212 ASP cc_start: 0.9060 (p0) cc_final: 0.8761 (p0) REVERT: E 364 ASN cc_start: 0.9031 (t0) cc_final: 0.8816 (t0) REVERT: E 373 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8821 (mmtp) REVERT: E 419 SER cc_start: 0.9550 (t) cc_final: 0.9304 (p) REVERT: F 351 TRP cc_start: 0.8344 (OUTLIER) cc_final: 0.7088 (m-90) outliers start: 146 outliers final: 121 residues processed: 376 average time/residue: 0.1557 time to fit residues: 90.0001 Evaluate side-chains 380 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 250 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 110 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 385 ASP Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain S residue 104 SER Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 349 THR Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 296 THR Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 351 TRP Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 46 ILE Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 255 optimal weight: 10.0000 chunk 250 optimal weight: 0.7980 chunk 154 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 224 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN E 100 ASN E 345 HIS E 362 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.056521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.041693 restraints weight = 62228.933| |-----------------------------------------------------------------------------| r_work (start): 0.2506 rms_B_bonded: 2.19 r_work: 0.2417 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2315 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9098 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22197 Z= 0.124 Angle : 0.608 13.966 30261 Z= 0.304 Chirality : 0.044 0.222 3393 Planarity : 0.005 0.072 3873 Dihedral : 5.294 51.017 3054 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.26 % Allowed : 27.33 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.15 (0.16), residues: 2790 helix: 1.11 (0.30), residues: 291 sheet: 0.33 (0.18), residues: 894 loop : -0.54 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 289 TYR 0.020 0.001 TYR F 328 PHE 0.028 0.001 PHE R 77 TRP 0.020 0.001 TRP E 409 HIS 0.009 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00289 (22140) covalent geometry : angle 0.60673 (30147) SS BOND : bond 0.00303 ( 57) SS BOND : angle 0.80073 ( 114) hydrogen bonds : bond 0.03386 ( 577) hydrogen bonds : angle 5.27469 ( 1521) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 251 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 2 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8886 (mt) REVERT: B 122 ASN cc_start: 0.9112 (m-40) cc_final: 0.8858 (m-40) REVERT: B 235 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.8531 (mttm) REVERT: B 393 ARG cc_start: 0.9087 (tpt170) cc_final: 0.8545 (tpt170) REVERT: B 396 CYS cc_start: 0.8739 (t) cc_final: 0.8452 (p) REVERT: B 397 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7919 (pp) REVERT: R 34 GLU cc_start: 0.8650 (pm20) cc_final: 0.8423 (pm20) REVERT: R 37 GLN cc_start: 0.9066 (mt0) cc_final: 0.8557 (mt0) REVERT: R 44 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.8069 (tmm-80) REVERT: C 21 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7687 (mtp85) REVERT: D 81 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.9109 (mt-10) REVERT: D 231 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8882 (mtt90) REVERT: D 393 ARG cc_start: 0.9463 (mmm-85) cc_final: 0.9044 (tpp80) REVERT: S 57 ASP cc_start: 0.8985 (t0) cc_final: 0.8728 (t0) REVERT: S 98 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8611 (pm20) REVERT: E 30 GLU cc_start: 0.8444 (tp30) cc_final: 0.8236 (tp30) REVERT: E 212 ASP cc_start: 0.9057 (p0) cc_final: 0.8725 (p0) REVERT: E 364 ASN cc_start: 0.8907 (t0) cc_final: 0.8694 (t0) REVERT: E 373 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8755 (mmtp) REVERT: E 419 SER cc_start: 0.9559 (t) cc_final: 0.9313 (p) REVERT: T 37 GLN cc_start: 0.9124 (mt0) cc_final: 0.8864 (mt0) outliers start: 102 outliers final: 88 residues processed: 336 average time/residue: 0.1646 time to fit residues: 84.4741 Evaluate side-chains 334 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 241 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 76 ASP Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 166 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 271 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 362 GLN C 100 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN E 100 ASN E 345 HIS E 362 GLN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.054752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.040038 restraints weight = 62135.537| |-----------------------------------------------------------------------------| r_work (start): 0.2427 rms_B_bonded: 2.15 r_work: 0.2335 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2234 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9129 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 22197 Z= 0.253 Angle : 0.676 13.611 30261 Z= 0.342 Chirality : 0.046 0.235 3393 Planarity : 0.005 0.073 3873 Dihedral : 5.598 49.786 3054 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.96 % Allowed : 26.78 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.18 (0.16), residues: 2790 helix: 1.07 (0.30), residues: 291 sheet: 0.34 (0.17), residues: 933 loop : -0.61 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 88 TYR 0.019 0.002 TYR A 308 PHE 0.031 0.002 PHE R 77 TRP 0.023 0.002 TRP E 409 HIS 0.013 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00595 (22140) covalent geometry : angle 0.67433 (30147) SS BOND : bond 0.00478 ( 57) SS BOND : angle 1.08183 ( 114) hydrogen bonds : bond 0.03915 ( 577) hydrogen bonds : angle 5.38631 ( 1521) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 252 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 2 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8886 (mt) REVERT: B 235 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.8604 (mttm) REVERT: B 393 ARG cc_start: 0.9107 (tpt170) cc_final: 0.8606 (tpt170) REVERT: B 396 CYS cc_start: 0.8840 (t) cc_final: 0.8578 (p) REVERT: B 397 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (pp) REVERT: R 34 GLU cc_start: 0.8665 (pm20) cc_final: 0.8455 (pm20) REVERT: R 37 GLN cc_start: 0.9031 (mt0) cc_final: 0.8466 (mt0) REVERT: R 44 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8140 (tmm-80) REVERT: C 21 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.6426 (mtp-110) REVERT: D 81 GLU cc_start: 0.9444 (OUTLIER) cc_final: 0.9134 (mt-10) REVERT: D 218 ASN cc_start: 0.8892 (m-40) cc_final: 0.8686 (m110) REVERT: D 231 ARG cc_start: 0.9145 (mtp85) cc_final: 0.8901 (mtt90) REVERT: D 393 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9089 (tpp80) REVERT: S 57 ASP cc_start: 0.9136 (t0) cc_final: 0.8872 (t0) REVERT: S 97 CYS cc_start: 0.6424 (t) cc_final: 0.6140 (t) REVERT: S 98 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8632 (pm20) REVERT: E 30 GLU cc_start: 0.8455 (tp30) cc_final: 0.8248 (tp30) REVERT: E 212 ASP cc_start: 0.9044 (p0) cc_final: 0.8740 (p0) REVERT: E 419 SER cc_start: 0.9549 (t) cc_final: 0.9299 (p) outliers start: 119 outliers final: 104 residues processed: 348 average time/residue: 0.1609 time to fit residues: 86.1860 Evaluate side-chains 352 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 242 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 214 GLN Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 126 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 261 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 GLN C 100 ASN ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.054103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.039463 restraints weight = 63032.946| |-----------------------------------------------------------------------------| r_work (start): 0.2409 rms_B_bonded: 2.18 r_work: 0.2314 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2213 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22197 Z= 0.295 Angle : 0.711 14.295 30261 Z= 0.360 Chirality : 0.047 0.241 3393 Planarity : 0.005 0.074 3873 Dihedral : 5.738 49.303 3054 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.17 % Allowed : 26.99 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.32 (0.16), residues: 2790 helix: 1.01 (0.30), residues: 291 sheet: 0.27 (0.17), residues: 906 loop : -0.71 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 88 TYR 0.025 0.002 TYR E 308 PHE 0.029 0.002 PHE R 77 TRP 0.024 0.002 TRP E 409 HIS 0.015 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00695 (22140) covalent geometry : angle 0.70880 (30147) SS BOND : bond 0.00517 ( 57) SS BOND : angle 1.11921 ( 114) hydrogen bonds : bond 0.04067 ( 577) hydrogen bonds : angle 5.48620 ( 1521) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5580 Ramachandran restraints generated. 2790 Oldfield, 0 Emsley, 2790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 243 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 327 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8116 (m-70) REVERT: A 345 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.7882 (m170) REVERT: B 2 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8885 (mt) REVERT: B 235 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.8625 (mttm) REVERT: B 393 ARG cc_start: 0.9102 (tpt170) cc_final: 0.8641 (tpt170) REVERT: B 396 CYS cc_start: 0.8831 (t) cc_final: 0.8561 (p) REVERT: B 397 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8009 (pp) REVERT: R 37 GLN cc_start: 0.9016 (mt0) cc_final: 0.8533 (mt0) REVERT: R 44 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: C 21 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7784 (mtp85) REVERT: D 81 GLU cc_start: 0.9470 (OUTLIER) cc_final: 0.9149 (mt-10) REVERT: D 218 ASN cc_start: 0.8941 (m-40) cc_final: 0.8641 (m110) REVERT: D 231 ARG cc_start: 0.9171 (mtp85) cc_final: 0.8883 (mtt90) REVERT: D 354 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: D 393 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9116 (tpp80) REVERT: S 57 ASP cc_start: 0.9186 (t0) cc_final: 0.8932 (t0) REVERT: S 98 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8554 (pm20) REVERT: E 30 GLU cc_start: 0.8492 (tp30) cc_final: 0.8247 (tp30) REVERT: E 212 ASP cc_start: 0.9062 (p0) cc_final: 0.8762 (p0) REVERT: E 347 THR cc_start: 0.8952 (p) cc_final: 0.8732 (t) REVERT: E 373 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8579 (mmmt) REVERT: E 419 SER cc_start: 0.9556 (t) cc_final: 0.9307 (p) outliers start: 124 outliers final: 106 residues processed: 347 average time/residue: 0.1527 time to fit residues: 81.1090 Evaluate side-chains 356 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 241 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 327 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 374 THR Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 1 SER Chi-restraints excluded: chain B residue 2 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 207 SER Chi-restraints excluded: chain B residue 213 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain R residue 36 SER Chi-restraints excluded: chain R residue 44 ARG Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 21 ARG Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 96 CYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 381 LYS Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 207 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 273 THR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 354 GLU Chi-restraints excluded: chain D residue 374 VAL Chi-restraints excluded: chain D residue 391 LYS Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain S residue 45 CYS Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain E residue 84 VAL Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 242 MET Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 381 LYS Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 205 ASP Chi-restraints excluded: chain F residue 224 ARG Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 ARG Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain T residue 71 THR Chi-restraints excluded: chain T residue 84 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 265 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 362 GLN ** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 345 HIS ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.055989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.041122 restraints weight = 62188.996| |-----------------------------------------------------------------------------| r_work (start): 0.2471 rms_B_bonded: 2.18 r_work: 0.2379 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2278 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22197 Z= 0.139 Angle : 0.632 14.749 30261 Z= 0.318 Chirality : 0.045 0.236 3393 Planarity : 0.005 0.072 3873 Dihedral : 5.375 50.529 3054 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.34 % Allowed : 27.66 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.16), residues: 2790 helix: 0.93 (0.30), residues: 291 sheet: 0.30 (0.18), residues: 909 loop : -0.56 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 88 TYR 0.020 0.001 TYR F 328 PHE 0.029 0.001 PHE R 77 TRP 0.016 0.001 TRP E 409 HIS 0.003 0.001 HIS B 256 Details of bonding type rmsd covalent geometry : bond 0.00326 (22140) covalent geometry : angle 0.62946 (30147) SS BOND : bond 0.00287 ( 57) SS BOND : angle 1.04655 ( 114) hydrogen bonds : bond 0.03464 ( 577) hydrogen bonds : angle 5.30043 ( 1521) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6114.11 seconds wall clock time: 105 minutes 19.22 seconds (6319.22 seconds total)