Starting phenix.real_space_refine on Fri Feb 6 01:55:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.map" model { file = "/net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wsl_66198/02_2026/9wsl_66198.cif" } resolution = 3.27 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= 0.004 sd= 0.028 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 23 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: 5.18, per 1000 atoms: 0.24 Number of scatterers: 21591 At special positions: 0 Unit cell: (163.2, 151.2, 177.6, 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=2.03 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=2.03 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=2.03 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=2.04 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=2.03 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=2.03 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: 1.61 Conformation dependent library (CDL) restraints added in 988.8 milliseconds 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: 39 helices and 69 sheets defined 14.6% alpha, 33.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.214A 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 403 through 439 Processing helix chain 'B' and resid 5 through 9 removed outlier: 3.551A 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: 4.233A pdb=" N GLY B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 414 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: 4.240A pdb=" N THR C 115 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 116 " --> pdb=" O ASP C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' 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: 4.380A pdb=" N ILE C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 422 " --> pdb=" O SER C 418 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.662A pdb=" N LEU D 8 " --> pdb=" O ASP D 5 " (cutoff:3.500A) 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: 4.233A pdb=" N GLY D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 415 removed outlier: 3.804A pdb=" N LEU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) 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 100 through 104 Processing helix chain 'E' and resid 112 through 116 removed outlier: 4.258A 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 289 through 293 Processing helix chain 'E' and resid 403 through 439 removed outlier: 3.527A pdb=" N MET E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 434 " --> pdb=" O CYS E 430 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E 439 " --> pdb=" O ILE E 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 removed outlier: 3.561A pdb=" N LEU F 8 " --> pdb=" O ASP F 5 " (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: 4.168A pdb=" N GLY F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 402 Proline residue: F 399 - end of helix Processing helix chain 'F' and resid 409 through 414 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 21 removed outlier: 5.632A pdb=" N ARG A 21 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 30 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.529A pdb=" N LEU A 144 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.529A pdb=" N LEU A 144 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 120 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL A 47 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A 45 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN A 43 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR A 126 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER A 35 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.650A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.578A pdb=" N GLN A 102 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL A 108 " --> pdb=" O ASP A 75 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ASP A 75 " --> pdb=" O VAL A 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AB1, first strand: chain 'A' and resid 296 through 302 removed outlier: 4.221A pdb=" N GLU A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB3, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB4, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.585A pdb=" N VAL B 336 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 282 " --> pdb=" O TRP B 279 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 387 through 388 removed outlier: 3.585A pdb=" N VAL B 336 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 291 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 311 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR B 293 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLU B 309 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 295 " --> pdb=" O THR B 307 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR B 307 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 14 through 16 Processing sheet with id=AB7, first strand: chain 'B' and resid 31 through 35 removed outlier: 8.550A pdb=" N ILE B 31 " --> pdb=" O SER B 48 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 48 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN B 33 " --> pdb=" O GLN B 46 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR B 99 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N ALA B 49 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LYS B 97 " --> pdb=" O ALA B 49 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N PHE B 51 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.860A pdb=" N GLY B 95 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 63 through 67 Processing sheet with id=AB9, first strand: chain 'B' and resid 83 through 86 removed outlier: 4.284A pdb=" N ASP B 109 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 148 through 155 Processing sheet with id=AC2, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.556A pdb=" N GLY B 253 " --> pdb=" O MET B 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 206 through 211 Processing sheet with id=AC4, first strand: chain 'R' and resid 37 through 39 Processing sheet with id=AC5, first strand: chain 'R' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AC7, first strand: chain 'C' and resid 7 through 8 Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 21 removed outlier: 5.331A pdb=" N ARG C 21 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 144 through 147 Processing sheet with id=AD1, first strand: chain 'C' and resid 144 through 147 removed outlier: 6.827A pdb=" N ALA C 119 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 47 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA C 121 " --> pdb=" O GLU C 45 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N SER C 41 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA C 127 " --> pdb=" O THR C 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C 39 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C 129 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C 37 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 131 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C 35 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 133 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 33 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD4, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD5, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD6, first strand: chain 'C' and resid 220 through 221 Processing sheet with id=AD7, first strand: chain 'C' and resid 296 through 302 removed outlier: 3.915A pdb=" N GLU C 298 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 3.520A pdb=" N VAL D 336 " --> pdb=" O TYR D 328 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 14 through 16 Processing sheet with id=AE2, first strand: chain 'D' and resid 31 through 35 removed outlier: 8.370A pdb=" N ILE D 31 " --> pdb=" O SER D 48 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER D 48 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ASN D 33 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR D 99 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N ALA D 49 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LYS D 97 " --> pdb=" O ALA D 49 " (cutoff:3.500A) removed outlier: 9.044A pdb=" N PHE D 51 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 11.007A pdb=" N GLY D 95 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 63 through 67 Processing sheet with id=AE4, first strand: chain 'D' and resid 83 through 86 removed outlier: 4.468A pdb=" N ASP D 109 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 148 through 155 Processing sheet with id=AE6, first strand: chain 'D' and resid 162 through 168 removed outlier: 6.221A pdb=" N ILE D 257 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR D 165 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU D 255 " --> pdb=" O TYR D 165 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N THR D 167 " --> pdb=" O GLY D 253 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY D 253 " --> pdb=" O THR D 167 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 206 through 211 Processing sheet with id=AE8, first strand: chain 'D' and resid 275 through 279 Processing sheet with id=AE9, first strand: chain 'S' and resid 37 through 39 Processing sheet with id=AF1, first strand: chain 'S' and resid 76 through 78 Processing sheet with id=AF2, first strand: chain 'E' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'E' and resid 15 through 21 removed outlier: 5.372A pdb=" N ARG E 21 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL E 136 " --> pdb=" O GLU E 30 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 33 through 48 removed outlier: 6.717A pdb=" N GLY E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS E 130 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 38 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR E 42 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 124 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS E 44 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 122 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR E 46 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 144 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 33 through 48 removed outlier: 6.717A pdb=" N GLY E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS E 130 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU E 38 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR E 42 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 124 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS E 44 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 122 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N TYR E 46 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.630A pdb=" N GLN E 59 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AF8, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF9, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AG1, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AG2, first strand: chain 'E' and resid 260 through 262 Processing sheet with id=AG3, first strand: chain 'E' and resid 296 through 302 removed outlier: 4.039A pdb=" N GLU E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 318 " --> pdb=" O ILE E 352 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 352 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY E 350 " --> pdb=" O TYR E 320 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AG5, first strand: chain 'E' and resid 387 through 388 removed outlier: 3.517A pdb=" N VAL F 336 " --> pdb=" O TYR F 328 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 387 through 388 removed outlier: 3.517A pdb=" N VAL F 336 " --> pdb=" O TYR F 328 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU F 285 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE F 319 " --> pdb=" O LEU F 285 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU F 287 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ARG F 317 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA F 289 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR F 315 " --> pdb=" O ALA F 289 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG F 291 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N GLY F 313 " --> pdb=" O ARG F 291 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AG8, first strand: chain 'F' and resid 31 through 35 removed outlier: 8.639A pdb=" N ILE F 31 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N SER F 48 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN F 33 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N ILE F 45 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 10.925A pdb=" N GLN F 104 " --> pdb=" O ILE F 45 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N VAL F 47 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 11.062A pdb=" N LEU F 102 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 9.160A pdb=" N ALA F 49 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N PHE F 100 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 98 " --> pdb=" O PHE F 51 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 63 through 67 Processing sheet with id=AH1, first strand: chain 'F' and resid 83 through 86 removed outlier: 5.948A pdb=" N LYS F 128 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N THR F 112 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N VAL F 126 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER F 114 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N CYS F 124 " --> pdb=" O SER F 114 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 149 through 155 Processing sheet with id=AH3, first strand: chain 'F' and resid 165 through 168 removed outlier: 3.601A pdb=" N GLY F 253 " --> pdb=" O MET F 168 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 207 through 211 Processing sheet with id=AH5, first strand: chain 'T' and resid 37 through 39 Processing sheet with id=AH6, first strand: chain 'T' and resid 76 through 78 722 hydrogen bonds defined for protein. 1905 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: 4.19 Time building geometry restraints manager: 2.24 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: 7032 1.34 - 1.46: 5188 1.46 - 1.58: 9728 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 22140 Sorted by residual: bond pdb=" CA ASP F 36 " pdb=" CB ASP F 36 " ideal model delta sigma weight residual 1.526 1.573 -0.047 1.70e-02 3.46e+03 7.68e+00 bond pdb=" C ASN D 239 " pdb=" N SER D 240 " ideal model delta sigma weight residual 1.331 1.286 0.045 2.83e-02 1.25e+03 2.55e+00 bond pdb=" CB ASP F 36 " pdb=" CG ASP F 36 " ideal model delta sigma weight residual 1.516 1.555 -0.039 2.50e-02 1.60e+03 2.49e+00 bond pdb=" CA PRO A 382 " pdb=" C PRO A 382 " ideal model delta sigma weight residual 1.517 1.508 0.009 6.70e-03 2.23e+04 1.77e+00 bond pdb=" CB ASP E 212 " pdb=" CG ASP E 212 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 22135 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 29738 2.31 - 4.62: 368 4.62 - 6.93: 25 6.93 - 9.24: 13 9.24 - 11.55: 3 Bond angle restraints: 30147 Sorted by residual: angle pdb=" C ASP F 36 " pdb=" CA ASP F 36 " pdb=" CB ASP F 36 " ideal model delta sigma weight residual 111.17 117.82 -6.65 1.54e+00 4.22e-01 1.86e+01 angle pdb=" N SER F 88 " pdb=" CA SER F 88 " pdb=" C SER F 88 " ideal model delta sigma weight residual 113.43 108.04 5.39 1.26e+00 6.30e-01 1.83e+01 angle pdb=" CA ASP F 36 " pdb=" CB ASP F 36 " pdb=" CG ASP F 36 " ideal model delta sigma weight residual 112.60 116.48 -3.88 1.00e+00 1.00e+00 1.51e+01 angle pdb=" N PRO D 348 " pdb=" CA PRO D 348 " pdb=" C PRO D 348 " ideal model delta sigma weight residual 114.68 111.02 3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" CA LEU F 402 " pdb=" CB LEU F 402 " pdb=" CG LEU F 402 " ideal model delta sigma weight residual 116.30 127.85 -11.55 3.50e+00 8.16e-02 1.09e+01 ... (remaining 30142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11389 17.99 - 35.97: 1555 35.97 - 53.96: 337 53.96 - 71.94: 71 71.94 - 89.93: 22 Dihedral angle restraints: 13374 sinusoidal: 5235 harmonic: 8139 Sorted by residual: dihedral pdb=" CB CYS T 72 " pdb=" SG CYS T 72 " pdb=" SG CYS T 84 " pdb=" CB CYS T 84 " ideal model delta sinusoidal sigma weight residual 93.00 178.11 -85.11 1 1.00e+01 1.00e-02 8.78e+01 dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 84 " pdb=" CB CYS R 84 " ideal model delta sinusoidal sigma weight residual 93.00 177.16 -84.16 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS S 40 " pdb=" SG CYS S 40 " pdb=" SG CYS S 58 " pdb=" CB CYS S 58 " ideal model delta sinusoidal sigma weight residual 93.00 164.39 -71.39 1 1.00e+01 1.00e-02 6.54e+01 ... (remaining 13371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2828 0.059 - 0.119: 526 0.119 - 0.178: 37 0.178 - 0.238: 0 0.238 - 0.297: 2 Chirality restraints: 3393 Sorted by residual: chirality pdb=" CG LEU B 371 " pdb=" CB LEU B 371 " pdb=" CD1 LEU B 371 " pdb=" CD2 LEU B 371 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CG LEU A 425 " pdb=" CB LEU A 425 " pdb=" CD1 LEU A 425 " pdb=" CD2 LEU A 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA ASP E 212 " pdb=" N ASP E 212 " pdb=" C ASP E 212 " pdb=" CB ASP E 212 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 3390 not shown) Planarity restraints: 3873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 36 " -0.015 2.00e-02 2.50e+03 2.91e-02 8.44e+00 pdb=" C ASP F 36 " 0.050 2.00e-02 2.50e+03 pdb=" O ASP F 36 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU F 37 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 381 " 0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C GLY B 381 " -0.041 2.00e-02 2.50e+03 pdb=" O GLY B 381 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 382 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 381 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.02e+00 pdb=" C GLY D 381 " -0.039 2.00e-02 2.50e+03 pdb=" O GLY D 381 " 0.014 2.00e-02 2.50e+03 pdb=" N THR D 382 " 0.013 2.00e-02 2.50e+03 ... (remaining 3870 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2892 2.75 - 3.29: 21162 3.29 - 3.83: 34870 3.83 - 4.36: 38964 4.36 - 4.90: 69198 Nonbonded interactions: 167086 Sorted by model distance: nonbonded pdb=" OD2 ASP R 102 " pdb="CA CA R 201 " model vdw 2.213 2.510 nonbonded pdb=" O ASP S 55 " pdb="CA CA S 202 " model vdw 2.237 2.510 nonbonded pdb=" OD1 ASP T 53 " pdb="CA CA T 202 " model vdw 2.242 2.510 nonbonded pdb=" OD2 ASP T 63 " pdb="CA CA T 202 " model vdw 2.243 2.510 nonbonded pdb=" O TRP R 89 " pdb="CA CA R 201 " model vdw 2.250 2.510 ... (remaining 167081 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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.020 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22197 Z= 0.228 Angle : 0.632 11.554 30261 Z= 0.329 Chirality : 0.044 0.297 3393 Planarity : 0.004 0.051 3873 Dihedral : 16.755 89.928 7971 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 3.00 % Allowed : 28.49 % 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: -0.17 (0.16), residues: 2790 helix: 1.29 (0.28), residues: 291 sheet: -0.32 (0.18), residues: 891 loop : -0.15 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 231 TYR 0.013 0.001 TYR A 273 PHE 0.015 0.001 PHE E 287 TRP 0.035 0.001 TRP E 409 HIS 0.012 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00511 (22140) covalent geometry : angle 0.63268 (30147) SS BOND : bond 0.00210 ( 57) SS BOND : angle 0.48647 ( 114) hydrogen bonds : bond 0.19294 ( 684) hydrogen bonds : angle 8.20356 ( 1905) *********************** 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 367 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 295 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.9437 (mtpp) cc_final: 0.9189 (mtpp) REVERT: A 218 ASP cc_start: 0.9101 (t0) cc_final: 0.8583 (t0) REVERT: A 246 ASN cc_start: 0.9332 (m-40) cc_final: 0.9065 (m-40) REVERT: A 320 TYR cc_start: 0.8450 (p90) cc_final: 0.7922 (p90) REVERT: A 328 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7851 (t) REVERT: A 411 LEU cc_start: 0.9325 (tp) cc_final: 0.9090 (tt) REVERT: B 55 GLN cc_start: 0.9474 (tt0) cc_final: 0.9165 (tm-30) REVERT: B 74 ASP cc_start: 0.8454 (t0) cc_final: 0.7956 (t0) REVERT: B 168 MET cc_start: 0.9173 (mmm) cc_final: 0.8236 (mmm) REVERT: B 217 MET cc_start: 0.7509 (tpp) cc_final: 0.7136 (tpp) REVERT: B 235 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8693 (mmmt) REVERT: B 303 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8596 (ttm-80) REVERT: B 369 ILE cc_start: 0.9037 (tp) cc_final: 0.8753 (tt) REVERT: C 30 GLU cc_start: 0.8428 (tp30) cc_final: 0.7912 (tp30) REVERT: C 52 HIS cc_start: 0.9203 (OUTLIER) cc_final: 0.8905 (t-90) REVERT: C 130 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8634 (tttp) REVERT: C 213 ILE cc_start: 0.9382 (mp) cc_final: 0.9113 (mp) REVERT: C 218 ASP cc_start: 0.9010 (t0) cc_final: 0.8291 (t0) REVERT: C 319 GLN cc_start: 0.9345 (mp10) cc_final: 0.9052 (mp10) REVERT: C 341 GLU cc_start: 0.8956 (mp0) cc_final: 0.8673 (mp0) REVERT: D 168 MET cc_start: 0.9215 (mmm) cc_final: 0.8529 (mmm) REVERT: D 217 MET cc_start: 0.7274 (tpp) cc_final: 0.6286 (tmm) REVERT: D 225 GLN cc_start: 0.8777 (mt0) cc_final: 0.8146 (pt0) REVERT: D 303 ARG cc_start: 0.8963 (ptp-110) cc_final: 0.8603 (ttp80) REVERT: D 388 CYS cc_start: 0.9498 (m) cc_final: 0.9242 (m) REVERT: D 393 ARG cc_start: 0.9358 (ttt180) cc_final: 0.8929 (ttt180) REVERT: S 63 ASP cc_start: 0.7895 (p0) cc_final: 0.7440 (p0) REVERT: S 99 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.6147 (p0) REVERT: S 109 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.6545 (t-90) REVERT: S 110 MET cc_start: 0.5586 (pmm) cc_final: 0.4537 (mpp) REVERT: E 37 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8232 (mm-30) REVERT: E 195 MET cc_start: 0.9291 (mpp) cc_final: 0.9083 (mpp) REVERT: E 218 ASP cc_start: 0.8854 (t0) cc_final: 0.8344 (t0) REVERT: E 319 GLN cc_start: 0.9272 (mm-40) cc_final: 0.9071 (tp40) REVERT: E 336 THR cc_start: 0.9573 (p) cc_final: 0.9325 (t) REVERT: E 341 GLU cc_start: 0.8470 (mp0) cc_final: 0.8213 (mp0) REVERT: E 366 ILE cc_start: 0.9599 (mm) cc_final: 0.9189 (tp) REVERT: E 398 PHE cc_start: 0.9304 (t80) cc_final: 0.8136 (m-10) REVERT: E 428 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8776 (mm) REVERT: E 439 ARG cc_start: 0.2492 (mmm160) cc_final: 0.1257 (ttt180) REVERT: F 122 ASN cc_start: 0.9197 (m110) cc_final: 0.8979 (m-40) REVERT: F 215 THR cc_start: 0.8627 (m) cc_final: 0.8305 (p) REVERT: F 217 MET cc_start: 0.8084 (tpp) cc_final: 0.7664 (tpp) REVERT: F 305 ASP cc_start: 0.9182 (m-30) cc_final: 0.8600 (t70) REVERT: T 110 MET cc_start: 0.4100 (mpp) cc_final: 0.3808 (mpp) outliers start: 72 outliers final: 61 residues processed: 350 average time/residue: 0.1464 time to fit residues: 80.5735 Evaluate side-chains 353 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 373 LYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 52 HIS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 344 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 47 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN A 43 ASN A 59 GLN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 235 GLN A 345 HIS ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 104 GLN B 174 HIS B 196 ASN B 225 GLN B 252 GLN B 318 ASN R 39 GLN R 42 ASN ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 HIS C 204 GLN D 174 HIS D 196 ASN D 225 GLN D 246 HIS D 252 GLN D 318 ASN D 332 ASN D 341 GLN S 37 GLN S 83 GLN E 3 HIS E 204 GLN ** E 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN F 73 HIS F 169 HIS F 196 ASN F 252 GLN F 318 ASN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN T 39 GLN T 83 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.070727 restraints weight = 44699.625| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.40 r_work: 0.2733 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22197 Z= 0.279 Angle : 0.594 8.874 30261 Z= 0.308 Chirality : 0.044 0.224 3393 Planarity : 0.004 0.046 3873 Dihedral : 6.520 59.263 3132 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 4.46 % Allowed : 25.41 % Favored : 70.13 % 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: -0.29 (0.16), residues: 2790 helix: 1.32 (0.28), residues: 291 sheet: -0.39 (0.17), residues: 918 loop : -0.27 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 438 TYR 0.015 0.001 TYR F 328 PHE 0.013 0.001 PHE B 142 TRP 0.021 0.001 TRP E 409 HIS 0.009 0.001 HIS B 96 Details of bonding type rmsd covalent geometry : bond 0.00629 (22140) covalent geometry : angle 0.59481 (30147) SS BOND : bond 0.00261 ( 57) SS BOND : angle 0.48786 ( 114) hydrogen bonds : bond 0.04227 ( 684) hydrogen bonds : angle 6.07944 ( 1905) *********************** 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 392 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 285 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.9355 (mtpp) cc_final: 0.9057 (mtpp) REVERT: A 218 ASP cc_start: 0.9079 (t0) cc_final: 0.8560 (t0) REVERT: A 246 ASN cc_start: 0.9380 (m-40) cc_final: 0.9107 (m-40) REVERT: A 328 CYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7580 (t) REVERT: A 411 LEU cc_start: 0.9307 (tp) cc_final: 0.9080 (tt) REVERT: B 33 ASN cc_start: 0.9155 (m-40) cc_final: 0.8889 (m-40) REVERT: B 138 GLU cc_start: 0.8892 (tt0) cc_final: 0.8547 (tp30) REVERT: B 168 MET cc_start: 0.9186 (mmm) cc_final: 0.8404 (mmm) REVERT: B 217 MET cc_start: 0.7500 (tpp) cc_final: 0.7270 (tpp) REVERT: B 232 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8339 (p0) REVERT: B 233 GLN cc_start: 0.8675 (mm110) cc_final: 0.8219 (mm-40) REVERT: B 252 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8986 (mm110) REVERT: B 303 ARG cc_start: 0.8883 (ttm-80) cc_final: 0.8565 (ttm-80) REVERT: B 369 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8698 (tt) REVERT: C 30 GLU cc_start: 0.8427 (tp30) cc_final: 0.7859 (tp30) REVERT: C 153 PRO cc_start: 0.9148 (Cg_endo) cc_final: 0.8902 (Cg_exo) REVERT: C 157 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8289 (tpm170) REVERT: C 204 GLN cc_start: 0.9449 (OUTLIER) cc_final: 0.9162 (pt0) REVERT: C 218 ASP cc_start: 0.9030 (t0) cc_final: 0.8241 (t0) REVERT: C 341 GLU cc_start: 0.8921 (mp0) cc_final: 0.8572 (mp0) REVERT: C 402 VAL cc_start: 0.8917 (t) cc_final: 0.8708 (m) REVERT: D 63 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8373 (mmmm) REVERT: D 168 MET cc_start: 0.9255 (mmm) cc_final: 0.8329 (mmm) REVERT: D 216 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8831 (tptp) REVERT: D 217 MET cc_start: 0.7229 (tpp) cc_final: 0.6068 (tmm) REVERT: D 225 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: D 303 ARG cc_start: 0.9004 (ptp-110) cc_final: 0.8550 (ttp80) REVERT: D 388 CYS cc_start: 0.9540 (m) cc_final: 0.9271 (m) REVERT: D 393 ARG cc_start: 0.9410 (ttt180) cc_final: 0.9140 (ttt180) REVERT: S 99 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6183 (p0) REVERT: E 37 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8344 (mm-30) REVERT: E 218 ASP cc_start: 0.8794 (t0) cc_final: 0.8297 (t0) REVERT: E 336 THR cc_start: 0.9500 (p) cc_final: 0.9236 (t) REVERT: E 341 GLU cc_start: 0.8399 (mp0) cc_final: 0.7774 (mp0) REVERT: E 366 ILE cc_start: 0.9589 (mm) cc_final: 0.9172 (tp) REVERT: E 395 ASP cc_start: 0.9085 (t70) cc_final: 0.8855 (t70) REVERT: E 396 GLN cc_start: 0.8815 (tt0) cc_final: 0.8584 (tt0) REVERT: E 398 PHE cc_start: 0.9279 (t80) cc_final: 0.7978 (m-10) REVERT: E 438 ARG cc_start: 0.7751 (mtp180) cc_final: 0.7539 (mtp180) REVERT: E 439 ARG cc_start: 0.2416 (mmm160) cc_final: 0.1235 (ttt180) REVERT: F 122 ASN cc_start: 0.9244 (m110) cc_final: 0.9018 (m-40) REVERT: F 215 THR cc_start: 0.8610 (m) cc_final: 0.8261 (p) REVERT: F 217 MET cc_start: 0.8289 (tpp) cc_final: 0.7798 (tpp) REVERT: F 305 ASP cc_start: 0.9181 (m-30) cc_final: 0.8512 (t70) REVERT: T 110 MET cc_start: 0.4107 (mpp) cc_final: 0.3794 (mpp) outliers start: 107 outliers final: 70 residues processed: 369 average time/residue: 0.1476 time to fit residues: 86.9603 Evaluate side-chains 352 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 273 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASP Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 355 ILE Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain T residue 109 HIS 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: 20.0000 chunk 203 optimal weight: 0.9980 chunk 149 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 0.4980 chunk 120 optimal weight: 20.0000 chunk 271 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 73 HIS B 225 GLN C 100 ASN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 341 GLN F 73 HIS F 341 GLN ** F 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.071450 restraints weight = 44348.281| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.43 r_work: 0.2762 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22197 Z= 0.148 Angle : 0.540 8.216 30261 Z= 0.274 Chirality : 0.043 0.250 3393 Planarity : 0.004 0.064 3873 Dihedral : 5.557 59.670 3081 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.23 % Rotamer: Outliers : 3.67 % Allowed : 25.78 % Favored : 70.55 % 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: 1.46 (0.28), residues: 291 sheet: -0.25 (0.17), residues: 912 loop : -0.20 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 21 TYR 0.016 0.001 TYR F 328 PHE 0.021 0.001 PHE R 77 TRP 0.018 0.001 TRP E 409 HIS 0.008 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00337 (22140) covalent geometry : angle 0.54035 (30147) SS BOND : bond 0.00181 ( 57) SS BOND : angle 0.44645 ( 114) hydrogen bonds : bond 0.03720 ( 684) hydrogen bonds : angle 5.52216 ( 1905) *********************** 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 375 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.9388 (mtpp) cc_final: 0.9109 (mtpp) REVERT: A 218 ASP cc_start: 0.9076 (t0) cc_final: 0.8575 (t0) REVERT: A 246 ASN cc_start: 0.9329 (m-40) cc_final: 0.9036 (m-40) REVERT: A 320 TYR cc_start: 0.8677 (p90) cc_final: 0.8196 (p90) REVERT: A 328 CYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7700 (t) REVERT: B 33 ASN cc_start: 0.9098 (m-40) cc_final: 0.8825 (m-40) REVERT: B 55 GLN cc_start: 0.9620 (tt0) cc_final: 0.9173 (tm-30) REVERT: B 74 ASP cc_start: 0.8742 (t0) cc_final: 0.8188 (t0) REVERT: B 135 VAL cc_start: 0.9306 (OUTLIER) cc_final: 0.9086 (m) REVERT: B 138 GLU cc_start: 0.8880 (tt0) cc_final: 0.8569 (tp30) REVERT: B 168 MET cc_start: 0.9124 (mmm) cc_final: 0.8335 (mmm) REVERT: B 217 MET cc_start: 0.7515 (tpp) cc_final: 0.7270 (tpp) REVERT: B 232 ASP cc_start: 0.8668 (p0) cc_final: 0.8247 (p0) REVERT: B 303 ARG cc_start: 0.8820 (ttm-80) cc_final: 0.8527 (ttm-80) REVERT: B 369 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8681 (tt) REVERT: R 77 PHE cc_start: 0.8667 (t80) cc_final: 0.8459 (t80) REVERT: C 30 GLU cc_start: 0.8405 (tp30) cc_final: 0.7835 (tp30) REVERT: C 153 PRO cc_start: 0.9132 (Cg_endo) cc_final: 0.8863 (Cg_exo) REVERT: C 218 ASP cc_start: 0.9014 (t0) cc_final: 0.8207 (t0) REVERT: C 341 GLU cc_start: 0.8941 (mp0) cc_final: 0.8596 (mp0) REVERT: D 168 MET cc_start: 0.9229 (mmm) cc_final: 0.8210 (mmm) REVERT: D 217 MET cc_start: 0.7241 (tpp) cc_final: 0.6899 (tpp) REVERT: D 225 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: D 303 ARG cc_start: 0.9007 (ptp-110) cc_final: 0.8546 (ttp80) REVERT: D 388 CYS cc_start: 0.9516 (m) cc_final: 0.9257 (m) REVERT: D 393 ARG cc_start: 0.9385 (ttt180) cc_final: 0.9123 (ttt180) REVERT: S 81 ASN cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (p0) REVERT: S 99 ASP cc_start: 0.6486 (OUTLIER) cc_final: 0.6235 (p0) REVERT: S 109 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6136 (t-90) REVERT: S 110 MET cc_start: 0.4971 (mpp) cc_final: 0.4025 (mmt) REVERT: E 37 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8314 (mm-30) REVERT: E 218 ASP cc_start: 0.8794 (t0) cc_final: 0.8258 (t0) REVERT: E 244 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9105 (ttmm) REVERT: E 336 THR cc_start: 0.9468 (p) cc_final: 0.9206 (t) REVERT: E 341 GLU cc_start: 0.8423 (mp0) cc_final: 0.7876 (mp0) REVERT: E 366 ILE cc_start: 0.9572 (mm) cc_final: 0.9134 (tp) REVERT: E 395 ASP cc_start: 0.9100 (t70) cc_final: 0.8883 (t70) REVERT: E 438 ARG cc_start: 0.7733 (mtp180) cc_final: 0.7312 (mtp180) REVERT: E 439 ARG cc_start: 0.2633 (mmm160) cc_final: 0.1326 (ttt180) REVERT: F 122 ASN cc_start: 0.9220 (m110) cc_final: 0.8983 (m-40) REVERT: F 195 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8924 (mmtm) REVERT: F 215 THR cc_start: 0.8577 (m) cc_final: 0.8239 (p) REVERT: F 217 MET cc_start: 0.8284 (tpp) cc_final: 0.7785 (tpp) REVERT: F 305 ASP cc_start: 0.9149 (m-30) cc_final: 0.8456 (t70) REVERT: T 110 MET cc_start: 0.4092 (mpp) cc_final: 0.3775 (mpp) outliers start: 88 outliers final: 60 residues processed: 355 average time/residue: 0.1533 time to fit residues: 86.6890 Evaluate side-chains 343 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 274 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain T residue 47 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 178 optimal weight: 8.9990 chunk 148 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 205 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 260 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 192 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN B 252 GLN C 204 GLN C 327 HIS D 225 GLN E 235 GLN F 73 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.107975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.070309 restraints weight = 44815.470| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.47 r_work: 0.2748 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22197 Z= 0.191 Angle : 0.546 8.545 30261 Z= 0.277 Chirality : 0.043 0.251 3393 Planarity : 0.004 0.066 3873 Dihedral : 5.448 58.247 3072 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 4.42 % Allowed : 24.91 % Favored : 70.67 % 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: -0.13 (0.16), residues: 2790 helix: 1.45 (0.28), residues: 291 sheet: -0.19 (0.17), residues: 882 loop : -0.23 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 21 TYR 0.015 0.001 TYR F 328 PHE 0.021 0.001 PHE R 77 TRP 0.021 0.001 TRP E 409 HIS 0.007 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00436 (22140) covalent geometry : angle 0.54637 (30147) SS BOND : bond 0.00211 ( 57) SS BOND : angle 0.43807 ( 114) hydrogen bonds : bond 0.03579 ( 684) hydrogen bonds : angle 5.32775 ( 1905) *********************** 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 381 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 275 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.9375 (mtpp) cc_final: 0.9095 (mtpp) REVERT: A 218 ASP cc_start: 0.9070 (t0) cc_final: 0.8562 (t0) REVERT: A 246 ASN cc_start: 0.9373 (m-40) cc_final: 0.9068 (m-40) REVERT: A 328 CYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7699 (t) REVERT: B 33 ASN cc_start: 0.9117 (m-40) cc_final: 0.8792 (m-40) REVERT: B 55 GLN cc_start: 0.9636 (tt0) cc_final: 0.9131 (tm-30) REVERT: B 74 ASP cc_start: 0.8727 (t0) cc_final: 0.8518 (t0) REVERT: B 138 GLU cc_start: 0.8892 (tt0) cc_final: 0.8570 (tp30) REVERT: B 168 MET cc_start: 0.9214 (mmm) cc_final: 0.8485 (mmm) REVERT: B 217 MET cc_start: 0.7454 (tpp) cc_final: 0.7143 (tpp) REVERT: B 232 ASP cc_start: 0.8640 (p0) cc_final: 0.8271 (p0) REVERT: B 233 GLN cc_start: 0.8685 (mm110) cc_final: 0.8279 (mm-40) REVERT: B 252 GLN cc_start: 0.9415 (OUTLIER) cc_final: 0.9086 (mm110) REVERT: B 303 ARG cc_start: 0.8835 (ttm-80) cc_final: 0.8555 (ttm-80) REVERT: B 369 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8670 (tt) REVERT: C 30 GLU cc_start: 0.8431 (tp30) cc_final: 0.7927 (tp30) REVERT: C 153 PRO cc_start: 0.9112 (Cg_endo) cc_final: 0.8820 (Cg_exo) REVERT: C 195 MET cc_start: 0.9564 (mpp) cc_final: 0.9138 (mpp) REVERT: C 204 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.8934 (pt0) REVERT: C 218 ASP cc_start: 0.8996 (t0) cc_final: 0.8162 (t0) REVERT: C 319 GLN cc_start: 0.9316 (mp10) cc_final: 0.8609 (mp10) REVERT: C 341 GLU cc_start: 0.8915 (mp0) cc_final: 0.8549 (mp0) REVERT: D 168 MET cc_start: 0.9233 (mmm) cc_final: 0.8597 (mmm) REVERT: D 217 MET cc_start: 0.7332 (tpp) cc_final: 0.7088 (tpp) REVERT: D 225 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8280 (pt0) REVERT: D 303 ARG cc_start: 0.9017 (ptp-110) cc_final: 0.8526 (ttp80) REVERT: D 324 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9007 (pm20) REVERT: D 388 CYS cc_start: 0.9518 (m) cc_final: 0.9237 (m) REVERT: D 393 ARG cc_start: 0.9468 (ttt180) cc_final: 0.9140 (ttt180) REVERT: S 81 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8664 (p0) REVERT: S 109 HIS cc_start: 0.7261 (OUTLIER) cc_final: 0.6096 (t-90) REVERT: S 110 MET cc_start: 0.5384 (mpp) cc_final: 0.4367 (mmt) REVERT: E 37 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8300 (mm-30) REVERT: E 218 ASP cc_start: 0.8776 (t0) cc_final: 0.8236 (t0) REVERT: E 244 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9083 (ttmm) REVERT: E 319 GLN cc_start: 0.8891 (tp40) cc_final: 0.8561 (tp40) REVERT: E 336 THR cc_start: 0.9446 (p) cc_final: 0.9187 (t) REVERT: E 341 GLU cc_start: 0.8468 (mp0) cc_final: 0.7927 (mp0) REVERT: E 362 GLN cc_start: 0.9173 (mm110) cc_final: 0.8955 (mm-40) REVERT: E 366 ILE cc_start: 0.9564 (mm) cc_final: 0.9133 (tp) REVERT: E 395 ASP cc_start: 0.9118 (t70) cc_final: 0.8884 (t70) REVERT: E 438 ARG cc_start: 0.8022 (mtp180) cc_final: 0.7716 (mtp180) REVERT: E 439 ARG cc_start: 0.2481 (mmm160) cc_final: 0.1491 (ttt180) REVERT: F 73 HIS cc_start: 0.9068 (t-90) cc_final: 0.8708 (t70) REVERT: F 122 ASN cc_start: 0.9231 (m110) cc_final: 0.8996 (m-40) REVERT: F 195 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8926 (mmtm) REVERT: F 215 THR cc_start: 0.8555 (m) cc_final: 0.8223 (p) REVERT: F 305 ASP cc_start: 0.9125 (m-30) cc_final: 0.8465 (t70) REVERT: T 110 MET cc_start: 0.4104 (mpp) cc_final: 0.3774 (mpp) outliers start: 106 outliers final: 72 residues processed: 360 average time/residue: 0.1469 time to fit residues: 84.0038 Evaluate side-chains 351 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 204 GLN Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 81 ASN Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Chi-restraints excluded: chain T residue 47 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 189 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 chunk 214 optimal weight: 20.0000 chunk 212 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 9 ASN ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN C 204 GLN C 345 HIS C 436 ASN D 225 GLN D 349 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.070505 restraints weight = 44713.325| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.46 r_work: 0.2751 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22197 Z= 0.180 Angle : 0.550 9.008 30261 Z= 0.276 Chirality : 0.043 0.282 3393 Planarity : 0.004 0.045 3873 Dihedral : 5.234 57.974 3064 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Rotamer: Outliers : 4.38 % Allowed : 25.28 % Favored : 70.34 % 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: -0.11 (0.16), residues: 2790 helix: 1.49 (0.28), residues: 291 sheet: -0.16 (0.18), residues: 882 loop : -0.24 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 231 TYR 0.015 0.001 TYR F 328 PHE 0.014 0.001 PHE B 142 TRP 0.020 0.001 TRP E 409 HIS 0.006 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00414 (22140) covalent geometry : angle 0.55052 (30147) SS BOND : bond 0.00206 ( 57) SS BOND : angle 0.49178 ( 114) hydrogen bonds : bond 0.03471 ( 684) hydrogen bonds : angle 5.17600 ( 1905) *********************** 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 386 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 281 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9011 (t80) cc_final: 0.8678 (t80) REVERT: A 30 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7657 (tm-30) REVERT: A 196 LYS cc_start: 0.9389 (mtpp) cc_final: 0.9112 (mtpp) REVERT: A 218 ASP cc_start: 0.9068 (t0) cc_final: 0.8576 (t0) REVERT: A 246 ASN cc_start: 0.9349 (m-40) cc_final: 0.9021 (m-40) REVERT: A 284 ASP cc_start: 0.8962 (OUTLIER) cc_final: 0.8748 (t0) REVERT: A 328 CYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7768 (t) REVERT: B 33 ASN cc_start: 0.9131 (m-40) cc_final: 0.8780 (m-40) REVERT: B 74 ASP cc_start: 0.8747 (t0) cc_final: 0.8469 (t0) REVERT: B 138 GLU cc_start: 0.8900 (tt0) cc_final: 0.8468 (tp30) REVERT: B 168 MET cc_start: 0.9211 (mmm) cc_final: 0.8467 (mmm) REVERT: B 232 ASP cc_start: 0.8597 (p0) cc_final: 0.8252 (p0) REVERT: B 233 GLN cc_start: 0.8629 (mm110) cc_final: 0.8257 (mm-40) REVERT: B 235 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8768 (mmmt) REVERT: B 303 ARG cc_start: 0.8849 (ttm-80) cc_final: 0.8568 (ttm-80) REVERT: C 30 GLU cc_start: 0.8428 (tp30) cc_final: 0.7953 (tp30) REVERT: C 153 PRO cc_start: 0.9118 (Cg_endo) cc_final: 0.8821 (Cg_exo) REVERT: C 218 ASP cc_start: 0.9000 (t0) cc_final: 0.8168 (t0) REVERT: C 319 GLN cc_start: 0.9306 (mp10) cc_final: 0.8615 (mp10) REVERT: C 341 GLU cc_start: 0.8917 (mp0) cc_final: 0.8567 (mp0) REVERT: D 168 MET cc_start: 0.9240 (mmm) cc_final: 0.8589 (mmm) REVERT: D 217 MET cc_start: 0.7393 (tpp) cc_final: 0.7127 (tpp) REVERT: D 225 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: D 303 ARG cc_start: 0.9037 (ptp-110) cc_final: 0.8545 (ttp80) REVERT: D 324 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.9012 (pm20) REVERT: D 388 CYS cc_start: 0.9516 (m) cc_final: 0.9235 (m) REVERT: D 393 ARG cc_start: 0.9453 (ttt180) cc_final: 0.9104 (ttt180) REVERT: S 109 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6254 (t-90) REVERT: E 37 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8189 (mm-30) REVERT: E 208 LEU cc_start: 0.9444 (mt) cc_final: 0.9239 (mt) REVERT: E 218 ASP cc_start: 0.8782 (t0) cc_final: 0.8255 (t0) REVERT: E 244 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.9098 (ttmm) REVERT: E 319 GLN cc_start: 0.8929 (tp40) cc_final: 0.8686 (tp40) REVERT: E 336 THR cc_start: 0.9447 (p) cc_final: 0.9204 (t) REVERT: E 341 GLU cc_start: 0.8519 (mp0) cc_final: 0.8011 (mp0) REVERT: E 366 ILE cc_start: 0.9558 (mm) cc_final: 0.9137 (tp) REVERT: E 395 ASP cc_start: 0.9110 (t70) cc_final: 0.8899 (t70) REVERT: E 397 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: E 438 ARG cc_start: 0.8134 (mtp180) cc_final: 0.7925 (mtp180) REVERT: E 439 ARG cc_start: 0.2240 (mmm160) cc_final: 0.1581 (ttt180) REVERT: F 122 ASN cc_start: 0.9239 (m110) cc_final: 0.8997 (m-40) REVERT: F 195 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: F 215 THR cc_start: 0.8552 (m) cc_final: 0.8235 (p) REVERT: F 217 MET cc_start: 0.8175 (tpp) cc_final: 0.7920 (tpp) REVERT: F 305 ASP cc_start: 0.9116 (m-30) cc_final: 0.8484 (t70) REVERT: T 110 MET cc_start: 0.4128 (mpp) cc_final: 0.3800 (mpp) outliers start: 105 outliers final: 73 residues processed: 365 average time/residue: 0.1446 time to fit residues: 84.0976 Evaluate side-chains 356 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 274 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 105 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 214 optimal weight: 30.0000 chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 266 optimal weight: 0.0970 chunk 225 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 190 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN C 100 ASN D 225 GLN D 341 GLN D 349 HIS F 73 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.069742 restraints weight = 44851.323| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.50 r_work: 0.2739 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22197 Z= 0.202 Angle : 0.567 9.940 30261 Z= 0.284 Chirality : 0.044 0.272 3393 Planarity : 0.004 0.045 3873 Dihedral : 5.237 57.257 3062 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.30 % Favored : 94.59 % Rotamer: Outliers : 4.38 % Allowed : 25.62 % Favored : 70.00 % 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: -0.14 (0.16), residues: 2790 helix: 1.44 (0.28), residues: 291 sheet: -0.18 (0.18), residues: 888 loop : -0.24 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 231 TYR 0.014 0.001 TYR F 328 PHE 0.013 0.001 PHE B 142 TRP 0.019 0.001 TRP E 409 HIS 0.008 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00462 (22140) covalent geometry : angle 0.56701 (30147) SS BOND : bond 0.00246 ( 57) SS BOND : angle 0.45200 ( 114) hydrogen bonds : bond 0.03473 ( 684) hydrogen bonds : angle 5.13992 ( 1905) *********************** 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 385 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 280 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9003 (t80) cc_final: 0.8651 (t80) REVERT: A 30 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7669 (tm-30) REVERT: A 196 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9111 (mtpp) REVERT: A 218 ASP cc_start: 0.9071 (t0) cc_final: 0.8573 (t0) REVERT: A 246 ASN cc_start: 0.9376 (m-40) cc_final: 0.9062 (m-40) REVERT: A 284 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8761 (t0) REVERT: A 328 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7990 (t) REVERT: B 33 ASN cc_start: 0.9095 (m-40) cc_final: 0.8706 (m-40) REVERT: B 55 GLN cc_start: 0.9588 (tt0) cc_final: 0.9089 (tp40) REVERT: B 74 ASP cc_start: 0.8757 (t0) cc_final: 0.8475 (t0) REVERT: B 138 GLU cc_start: 0.8912 (tt0) cc_final: 0.8477 (tp30) REVERT: B 168 MET cc_start: 0.9206 (mmm) cc_final: 0.8469 (mmm) REVERT: B 217 MET cc_start: 0.7494 (tpp) cc_final: 0.7223 (tpp) REVERT: B 232 ASP cc_start: 0.8619 (p0) cc_final: 0.8289 (p0) REVERT: B 233 GLN cc_start: 0.8601 (mm110) cc_final: 0.8262 (mm-40) REVERT: B 235 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8767 (mmmt) REVERT: B 303 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8580 (ttm-80) REVERT: B 324 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8860 (pm20) REVERT: C 30 GLU cc_start: 0.8436 (tp30) cc_final: 0.7955 (tp30) REVERT: C 153 PRO cc_start: 0.9120 (Cg_endo) cc_final: 0.8843 (Cg_exo) REVERT: C 160 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9123 (mmmm) REVERT: C 213 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.9016 (mp) REVERT: C 218 ASP cc_start: 0.9003 (t0) cc_final: 0.8164 (t0) REVERT: C 319 GLN cc_start: 0.9311 (mp10) cc_final: 0.8398 (mp10) REVERT: C 341 GLU cc_start: 0.8935 (mp0) cc_final: 0.8566 (mp0) REVERT: D 168 MET cc_start: 0.9239 (mmm) cc_final: 0.8538 (mmm) REVERT: D 217 MET cc_start: 0.7365 (tpp) cc_final: 0.7087 (tpp) REVERT: D 225 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: D 303 ARG cc_start: 0.8946 (ptp-110) cc_final: 0.8480 (ttp80) REVERT: D 324 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.9015 (pm20) REVERT: D 348 PRO cc_start: 0.9358 (Cg_endo) cc_final: 0.9101 (Cg_exo) REVERT: D 388 CYS cc_start: 0.9522 (m) cc_final: 0.9230 (m) REVERT: D 393 ARG cc_start: 0.9452 (ttt180) cc_final: 0.9228 (ttt180) REVERT: D 396 CYS cc_start: 0.9643 (OUTLIER) cc_final: 0.9411 (p) REVERT: S 109 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6267 (t-90) REVERT: S 110 MET cc_start: 0.5378 (mpp) cc_final: 0.4421 (mmt) REVERT: E 16 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9334 (mmmm) REVERT: E 37 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8238 (mm-30) REVERT: E 208 LEU cc_start: 0.9460 (mt) cc_final: 0.9241 (mt) REVERT: E 218 ASP cc_start: 0.8782 (t0) cc_final: 0.8236 (t0) REVERT: E 244 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9092 (ttmm) REVERT: E 319 GLN cc_start: 0.8889 (tp40) cc_final: 0.8650 (tp40) REVERT: E 336 THR cc_start: 0.9433 (p) cc_final: 0.9192 (t) REVERT: E 341 GLU cc_start: 0.8523 (mp0) cc_final: 0.8001 (mp0) REVERT: E 366 ILE cc_start: 0.9549 (mm) cc_final: 0.9135 (tp) REVERT: E 395 ASP cc_start: 0.9117 (t70) cc_final: 0.8856 (t70) REVERT: E 397 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: F 73 HIS cc_start: 0.9066 (t-90) cc_final: 0.8707 (t70) REVERT: F 122 ASN cc_start: 0.9245 (m110) cc_final: 0.9017 (m-40) REVERT: F 195 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8934 (mmtm) REVERT: F 215 THR cc_start: 0.8551 (m) cc_final: 0.8227 (p) REVERT: F 217 MET cc_start: 0.8208 (tpp) cc_final: 0.7930 (tpp) REVERT: F 305 ASP cc_start: 0.9108 (m-30) cc_final: 0.8486 (t70) REVERT: T 110 MET cc_start: 0.4130 (mpp) cc_final: 0.3763 (mpp) outliers start: 105 outliers final: 77 residues processed: 364 average time/residue: 0.1441 time to fit residues: 83.4178 Evaluate side-chains 366 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 275 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 396 CYS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 246 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN B 252 GLN C 345 HIS D 225 GLN D 349 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.070337 restraints weight = 44509.312| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.48 r_work: 0.2753 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22197 Z= 0.154 Angle : 0.573 11.621 30261 Z= 0.285 Chirality : 0.043 0.302 3393 Planarity : 0.004 0.045 3873 Dihedral : 5.197 57.560 3062 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Rotamer: Outliers : 4.21 % Allowed : 25.95 % Favored : 69.84 % 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: -0.09 (0.16), residues: 2790 helix: 1.48 (0.28), residues: 291 sheet: -0.12 (0.18), residues: 885 loop : -0.23 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 231 TYR 0.014 0.001 TYR F 328 PHE 0.012 0.001 PHE B 142 TRP 0.019 0.001 TRP E 409 HIS 0.008 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00360 (22140) covalent geometry : angle 0.57235 (30147) SS BOND : bond 0.00210 ( 57) SS BOND : angle 0.78737 ( 114) hydrogen bonds : bond 0.03366 ( 684) hydrogen bonds : angle 5.04615 ( 1905) *********************** 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 392 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 291 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9009 (t80) cc_final: 0.8646 (t80) REVERT: A 30 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 196 LYS cc_start: 0.9393 (mtpp) cc_final: 0.9121 (mtpp) REVERT: A 218 ASP cc_start: 0.9070 (t0) cc_final: 0.8582 (t0) REVERT: A 228 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8665 (p0) REVERT: A 246 ASN cc_start: 0.9335 (m-40) cc_final: 0.9012 (m-40) REVERT: A 284 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8776 (t0) REVERT: B 33 ASN cc_start: 0.9088 (m-40) cc_final: 0.8694 (m-40) REVERT: B 55 GLN cc_start: 0.9598 (tt0) cc_final: 0.9121 (tp40) REVERT: B 74 ASP cc_start: 0.8733 (t0) cc_final: 0.8375 (t0) REVERT: B 138 GLU cc_start: 0.8888 (tt0) cc_final: 0.8577 (tp30) REVERT: B 168 MET cc_start: 0.9206 (mmm) cc_final: 0.8470 (mmm) REVERT: B 217 MET cc_start: 0.7730 (tpp) cc_final: 0.7430 (tpp) REVERT: B 235 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8770 (mmmt) REVERT: B 252 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9031 (mm-40) REVERT: B 303 ARG cc_start: 0.8858 (ttm-80) cc_final: 0.8571 (ttm-80) REVERT: C 30 GLU cc_start: 0.8381 (tp30) cc_final: 0.7910 (tp30) REVERT: C 153 PRO cc_start: 0.9116 (Cg_endo) cc_final: 0.8824 (Cg_exo) REVERT: C 160 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.9129 (mmmm) REVERT: C 218 ASP cc_start: 0.9001 (t0) cc_final: 0.8166 (t0) REVERT: C 319 GLN cc_start: 0.9303 (mp10) cc_final: 0.8414 (mp10) REVERT: C 341 GLU cc_start: 0.8916 (mp0) cc_final: 0.8522 (mp0) REVERT: D 168 MET cc_start: 0.9245 (mmm) cc_final: 0.8566 (mmm) REVERT: D 217 MET cc_start: 0.7391 (tpp) cc_final: 0.7096 (tpp) REVERT: D 225 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: D 303 ARG cc_start: 0.9014 (ptp-110) cc_final: 0.8542 (ttp80) REVERT: D 324 GLU cc_start: 0.9267 (OUTLIER) cc_final: 0.9009 (pm20) REVERT: D 348 PRO cc_start: 0.9315 (Cg_endo) cc_final: 0.9085 (Cg_exo) REVERT: D 388 CYS cc_start: 0.9512 (m) cc_final: 0.9222 (m) REVERT: D 393 ARG cc_start: 0.9440 (ttt180) cc_final: 0.9204 (ttt180) REVERT: D 396 CYS cc_start: 0.9612 (OUTLIER) cc_final: 0.9375 (p) REVERT: S 109 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.6257 (t-90) REVERT: S 110 MET cc_start: 0.5417 (mpp) cc_final: 0.4479 (mmt) REVERT: E 16 LYS cc_start: 0.9563 (OUTLIER) cc_final: 0.9335 (mmmm) REVERT: E 37 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8193 (mm-30) REVERT: E 208 LEU cc_start: 0.9438 (mt) cc_final: 0.9222 (mt) REVERT: E 218 ASP cc_start: 0.8774 (t0) cc_final: 0.8235 (t0) REVERT: E 244 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9102 (ttmm) REVERT: E 319 GLN cc_start: 0.8946 (tp40) cc_final: 0.8730 (tp40) REVERT: E 336 THR cc_start: 0.9409 (p) cc_final: 0.9159 (t) REVERT: E 341 GLU cc_start: 0.8543 (mp0) cc_final: 0.7977 (mp0) REVERT: E 366 ILE cc_start: 0.9547 (mm) cc_final: 0.9118 (tp) REVERT: E 395 ASP cc_start: 0.9121 (t70) cc_final: 0.8850 (t70) REVERT: E 397 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: E 430 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7756 (p) REVERT: E 439 ARG cc_start: 0.2122 (mmm160) cc_final: 0.1563 (ttt180) REVERT: F 122 ASN cc_start: 0.9235 (m110) cc_final: 0.8990 (m-40) REVERT: F 195 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: F 215 THR cc_start: 0.8539 (m) cc_final: 0.8218 (p) REVERT: F 217 MET cc_start: 0.8182 (tpp) cc_final: 0.7839 (tpp) REVERT: F 305 ASP cc_start: 0.9090 (m-30) cc_final: 0.8425 (t70) REVERT: T 110 MET cc_start: 0.4134 (mpp) cc_final: 0.3768 (mpp) outliers start: 101 outliers final: 71 residues processed: 374 average time/residue: 0.1438 time to fit residues: 85.8444 Evaluate side-chains 371 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 286 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 252 GLN Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 396 CYS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 202 optimal weight: 7.9990 chunk 255 optimal weight: 9.9990 chunk 250 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN C 364 ASN D 225 GLN D 349 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.071508 restraints weight = 44087.973| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.41 r_work: 0.2769 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22197 Z= 0.144 Angle : 0.573 12.869 30261 Z= 0.282 Chirality : 0.044 0.316 3393 Planarity : 0.004 0.046 3873 Dihedral : 5.111 57.372 3060 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.77 % Rotamer: Outliers : 3.92 % Allowed : 26.57 % Favored : 69.50 % 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: -0.07 (0.16), residues: 2790 helix: 1.47 (0.28), residues: 291 sheet: -0.09 (0.18), residues: 885 loop : -0.22 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 231 TYR 0.014 0.001 TYR F 328 PHE 0.011 0.001 PHE B 142 TRP 0.017 0.001 TRP E 409 HIS 0.006 0.001 HIS D 349 Details of bonding type rmsd covalent geometry : bond 0.00336 (22140) covalent geometry : angle 0.57374 (30147) SS BOND : bond 0.00167 ( 57) SS BOND : angle 0.40991 ( 114) hydrogen bonds : bond 0.03305 ( 684) hydrogen bonds : angle 4.98303 ( 1905) *********************** 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 384 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 290 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9030 (t80) cc_final: 0.8715 (t80) REVERT: A 30 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7784 (tm-30) REVERT: A 196 LYS cc_start: 0.9386 (mtpp) cc_final: 0.9112 (mtpp) REVERT: A 218 ASP cc_start: 0.9069 (t0) cc_final: 0.8584 (t0) REVERT: A 228 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8645 (p0) REVERT: A 246 ASN cc_start: 0.9335 (m-40) cc_final: 0.9000 (m-40) REVERT: B 33 ASN cc_start: 0.9089 (m-40) cc_final: 0.8680 (m-40) REVERT: B 55 GLN cc_start: 0.9599 (tt0) cc_final: 0.9109 (tp40) REVERT: B 74 ASP cc_start: 0.8749 (t0) cc_final: 0.8367 (t0) REVERT: B 138 GLU cc_start: 0.8883 (tt0) cc_final: 0.8572 (tp30) REVERT: B 168 MET cc_start: 0.9228 (mmm) cc_final: 0.8352 (mmm) REVERT: B 217 MET cc_start: 0.7664 (tpp) cc_final: 0.7464 (tpp) REVERT: B 235 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8730 (mmmt) REVERT: B 303 ARG cc_start: 0.8870 (ttm-80) cc_final: 0.8586 (ttm-80) REVERT: C 30 GLU cc_start: 0.8373 (tp30) cc_final: 0.7909 (tp30) REVERT: C 153 PRO cc_start: 0.9104 (Cg_endo) cc_final: 0.8807 (Cg_exo) REVERT: C 160 LYS cc_start: 0.9471 (mmmt) cc_final: 0.9099 (mmmm) REVERT: C 218 ASP cc_start: 0.8998 (t0) cc_final: 0.8166 (t0) REVERT: C 319 GLN cc_start: 0.9298 (mp10) cc_final: 0.8407 (mp10) REVERT: C 341 GLU cc_start: 0.8911 (mp0) cc_final: 0.8574 (mp0) REVERT: D 36 ASP cc_start: 0.9185 (p0) cc_final: 0.8961 (p0) REVERT: D 168 MET cc_start: 0.9242 (mmm) cc_final: 0.8564 (mmm) REVERT: D 217 MET cc_start: 0.7327 (tpp) cc_final: 0.7028 (tpp) REVERT: D 225 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: D 303 ARG cc_start: 0.9012 (ptp-110) cc_final: 0.8538 (ttp80) REVERT: D 347 ASP cc_start: 0.9189 (t0) cc_final: 0.8756 (t0) REVERT: D 388 CYS cc_start: 0.9509 (m) cc_final: 0.9217 (m) REVERT: D 393 ARG cc_start: 0.9430 (ttt180) cc_final: 0.9189 (ttt180) REVERT: D 396 CYS cc_start: 0.9590 (OUTLIER) cc_final: 0.9339 (p) REVERT: S 109 HIS cc_start: 0.7418 (OUTLIER) cc_final: 0.6194 (t-90) REVERT: S 110 MET cc_start: 0.5551 (mpp) cc_final: 0.4617 (mmt) REVERT: E 16 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9335 (mmmm) REVERT: E 37 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8161 (mm-30) REVERT: E 208 LEU cc_start: 0.9433 (mt) cc_final: 0.9230 (mt) REVERT: E 218 ASP cc_start: 0.8766 (t0) cc_final: 0.8051 (t0) REVERT: E 244 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9102 (ttmm) REVERT: E 319 GLN cc_start: 0.8942 (tp40) cc_final: 0.8718 (tp40) REVERT: E 341 GLU cc_start: 0.8537 (mp0) cc_final: 0.8020 (mp0) REVERT: E 366 ILE cc_start: 0.9542 (mm) cc_final: 0.9105 (tp) REVERT: E 395 ASP cc_start: 0.9097 (t70) cc_final: 0.8819 (t70) REVERT: E 397 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: E 430 CYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7733 (p) REVERT: E 438 ARG cc_start: 0.7675 (mtp180) cc_final: 0.7407 (ptm160) REVERT: E 439 ARG cc_start: 0.2305 (mmm160) cc_final: 0.1441 (ttt180) REVERT: F 80 MET cc_start: 0.9120 (mmm) cc_final: 0.8326 (tmm) REVERT: F 122 ASN cc_start: 0.9218 (m110) cc_final: 0.8973 (m-40) REVERT: F 195 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8928 (mmtm) REVERT: F 215 THR cc_start: 0.8542 (m) cc_final: 0.8223 (p) REVERT: F 217 MET cc_start: 0.8130 (tpp) cc_final: 0.7756 (tpp) REVERT: F 305 ASP cc_start: 0.9067 (m-30) cc_final: 0.8412 (t70) REVERT: T 110 MET cc_start: 0.4100 (mpp) cc_final: 0.3724 (mpp) outliers start: 94 outliers final: 74 residues processed: 367 average time/residue: 0.1443 time to fit residues: 84.5464 Evaluate side-chains 365 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 225 GLN Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 396 CYS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 166 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN D 225 GLN D 349 HIS ** F 73 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 = 0.3524 r_free = 0.3524 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.071718 restraints weight = 43910.405| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.41 r_work: 0.2773 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22197 Z= 0.144 Angle : 0.582 11.952 30261 Z= 0.286 Chirality : 0.044 0.310 3393 Planarity : 0.004 0.047 3873 Dihedral : 5.127 57.264 3060 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 3.59 % Allowed : 26.70 % Favored : 69.71 % 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: -0.05 (0.16), residues: 2790 helix: 1.48 (0.29), residues: 291 sheet: -0.04 (0.18), residues: 864 loop : -0.24 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 20 TYR 0.013 0.001 TYR F 328 PHE 0.024 0.001 PHE B 142 TRP 0.015 0.001 TRP R 89 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00338 (22140) covalent geometry : angle 0.58166 (30147) SS BOND : bond 0.00172 ( 57) SS BOND : angle 0.67814 ( 114) hydrogen bonds : bond 0.03279 ( 684) hydrogen bonds : angle 4.95822 ( 1905) *********************** 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 382 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 296 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9031 (t80) cc_final: 0.8710 (t80) REVERT: A 30 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7732 (tm-30) REVERT: A 196 LYS cc_start: 0.9387 (mtpp) cc_final: 0.9108 (mtpp) REVERT: A 218 ASP cc_start: 0.9074 (t0) cc_final: 0.8590 (t0) REVERT: A 228 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.8630 (p0) REVERT: B 33 ASN cc_start: 0.9094 (m-40) cc_final: 0.8681 (m-40) REVERT: B 55 GLN cc_start: 0.9607 (tt0) cc_final: 0.9138 (tp40) REVERT: B 74 ASP cc_start: 0.8762 (t0) cc_final: 0.8375 (t0) REVERT: B 138 GLU cc_start: 0.8885 (tt0) cc_final: 0.8585 (tp30) REVERT: B 168 MET cc_start: 0.9206 (mmm) cc_final: 0.8454 (mmm) REVERT: B 217 MET cc_start: 0.7653 (tpp) cc_final: 0.7443 (tpp) REVERT: B 235 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8739 (mmmt) REVERT: B 303 ARG cc_start: 0.8861 (ttm-80) cc_final: 0.8576 (ttm-80) REVERT: C 30 GLU cc_start: 0.8374 (tp30) cc_final: 0.7912 (tp30) REVERT: C 153 PRO cc_start: 0.9103 (Cg_endo) cc_final: 0.8803 (Cg_exo) REVERT: C 160 LYS cc_start: 0.9462 (mmmt) cc_final: 0.9104 (mmmm) REVERT: C 218 ASP cc_start: 0.8988 (t0) cc_final: 0.8173 (t0) REVERT: C 319 GLN cc_start: 0.9293 (mp10) cc_final: 0.8402 (mp10) REVERT: C 341 GLU cc_start: 0.8908 (mp0) cc_final: 0.8569 (mp0) REVERT: D 168 MET cc_start: 0.9241 (mmm) cc_final: 0.8549 (mmm) REVERT: D 217 MET cc_start: 0.7194 (tpp) cc_final: 0.6854 (tpp) REVERT: D 225 GLN cc_start: 0.8762 (mt0) cc_final: 0.8350 (pt0) REVERT: D 303 ARG cc_start: 0.9013 (ptp-110) cc_final: 0.8534 (ttp80) REVERT: D 347 ASP cc_start: 0.9162 (t0) cc_final: 0.8766 (t0) REVERT: D 388 CYS cc_start: 0.9509 (m) cc_final: 0.9217 (m) REVERT: D 393 ARG cc_start: 0.9425 (ttt180) cc_final: 0.9181 (ttt180) REVERT: D 396 CYS cc_start: 0.9588 (OUTLIER) cc_final: 0.9337 (p) REVERT: S 109 HIS cc_start: 0.7405 (OUTLIER) cc_final: 0.6201 (t-90) REVERT: S 110 MET cc_start: 0.5563 (mpp) cc_final: 0.4680 (mmt) REVERT: E 16 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.9341 (mmmm) REVERT: E 37 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8227 (mm-30) REVERT: E 208 LEU cc_start: 0.9434 (mt) cc_final: 0.9233 (mt) REVERT: E 218 ASP cc_start: 0.8764 (t0) cc_final: 0.8048 (t0) REVERT: E 244 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9103 (ttmm) REVERT: E 264 GLU cc_start: 0.9188 (mp0) cc_final: 0.8987 (mp0) REVERT: E 319 GLN cc_start: 0.8940 (tp40) cc_final: 0.8719 (tp40) REVERT: E 341 GLU cc_start: 0.8553 (mp0) cc_final: 0.8036 (mp0) REVERT: E 366 ILE cc_start: 0.9552 (mm) cc_final: 0.9103 (tp) REVERT: E 395 ASP cc_start: 0.9103 (t70) cc_final: 0.8824 (t70) REVERT: E 397 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: E 430 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7714 (p) REVERT: E 439 ARG cc_start: 0.2284 (mmm160) cc_final: 0.1397 (ttt180) REVERT: F 122 ASN cc_start: 0.9208 (m110) cc_final: 0.8963 (m-40) REVERT: F 195 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8924 (mmtm) REVERT: F 215 THR cc_start: 0.8511 (m) cc_final: 0.8177 (p) REVERT: F 217 MET cc_start: 0.8143 (tpp) cc_final: 0.7758 (tpp) REVERT: F 231 ARG cc_start: 0.8523 (mmm160) cc_final: 0.8159 (mmm160) REVERT: F 305 ASP cc_start: 0.9067 (m-30) cc_final: 0.8413 (t70) REVERT: F 343 SER cc_start: 0.8955 (t) cc_final: 0.8348 (p) REVERT: T 110 MET cc_start: 0.4011 (mpp) cc_final: 0.3601 (mpp) outliers start: 86 outliers final: 69 residues processed: 367 average time/residue: 0.1474 time to fit residues: 85.9593 Evaluate side-chains 368 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 290 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 228 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 80 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 349 HIS Chi-restraints excluded: chain D residue 396 CYS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 126 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 157 optimal weight: 0.0170 chunk 189 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 4.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 HIS B 225 GLN D 349 HIS F 73 HIS ** F 349 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 = 0.3516 r_free = 0.3516 target = 0.107692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.070019 restraints weight = 45146.897| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.47 r_work: 0.2743 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 22197 Z= 0.231 Angle : 0.622 11.607 30261 Z= 0.309 Chirality : 0.045 0.314 3393 Planarity : 0.004 0.046 3873 Dihedral : 5.242 55.865 3057 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.59 % Favored : 94.34 % Rotamer: Outliers : 3.59 % Allowed : 26.78 % Favored : 69.63 % 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: 1.39 (0.28), residues: 291 sheet: -0.17 (0.18), residues: 870 loop : -0.31 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 20 TYR 0.014 0.001 TYR F 328 PHE 0.022 0.001 PHE B 142 TRP 0.013 0.001 TRP R 89 HIS 0.005 0.001 HIS B 71 Details of bonding type rmsd covalent geometry : bond 0.00532 (22140) covalent geometry : angle 0.61929 (30147) SS BOND : bond 0.00276 ( 57) SS BOND : angle 1.16233 ( 114) hydrogen bonds : bond 0.03452 ( 684) hydrogen bonds : angle 5.03844 ( 1905) ********************** 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 373 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 287 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 TYR cc_start: 0.9050 (t80) cc_final: 0.8768 (t80) REVERT: A 30 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7756 (tm-30) REVERT: A 196 LYS cc_start: 0.9408 (mtpp) cc_final: 0.9137 (mtpp) REVERT: A 218 ASP cc_start: 0.9086 (t0) cc_final: 0.8603 (t0) REVERT: A 246 ASN cc_start: 0.9386 (m-40) cc_final: 0.9081 (m-40) REVERT: B 33 ASN cc_start: 0.9121 (m-40) cc_final: 0.8729 (m-40) REVERT: B 55 GLN cc_start: 0.9622 (tt0) cc_final: 0.9077 (tp40) REVERT: B 74 ASP cc_start: 0.8811 (t0) cc_final: 0.8448 (t0) REVERT: B 138 GLU cc_start: 0.8890 (tt0) cc_final: 0.8470 (tp30) REVERT: B 168 MET cc_start: 0.9249 (mmm) cc_final: 0.8340 (mmm) REVERT: B 217 MET cc_start: 0.7638 (tpp) cc_final: 0.7432 (tpp) REVERT: B 235 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.8767 (mmmt) REVERT: B 303 ARG cc_start: 0.8890 (ttm-80) cc_final: 0.8514 (ttm110) REVERT: B 324 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (pm20) REVERT: C 30 GLU cc_start: 0.8385 (tp30) cc_final: 0.7936 (tp30) REVERT: C 160 LYS cc_start: 0.9492 (mmmt) cc_final: 0.9135 (mmmm) REVERT: C 218 ASP cc_start: 0.9021 (t0) cc_final: 0.8212 (t0) REVERT: C 319 GLN cc_start: 0.9308 (mp10) cc_final: 0.8414 (mp10) REVERT: C 341 GLU cc_start: 0.8963 (mp0) cc_final: 0.8619 (mp0) REVERT: D 168 MET cc_start: 0.9222 (mmm) cc_final: 0.8422 (mmm) REVERT: D 225 GLN cc_start: 0.8767 (mt0) cc_final: 0.8362 (pt0) REVERT: D 303 ARG cc_start: 0.8971 (ptp-110) cc_final: 0.8503 (ttp80) REVERT: D 347 ASP cc_start: 0.9191 (t0) cc_final: 0.8695 (t0) REVERT: D 388 CYS cc_start: 0.9517 (m) cc_final: 0.9264 (m) REVERT: D 393 ARG cc_start: 0.9432 (ttt180) cc_final: 0.9193 (ttt180) REVERT: D 396 CYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9329 (p) REVERT: S 109 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6225 (t-90) REVERT: S 110 MET cc_start: 0.5599 (mpp) cc_final: 0.4734 (mmt) REVERT: E 16 LYS cc_start: 0.9570 (OUTLIER) cc_final: 0.9356 (mmmm) REVERT: E 37 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8191 (mm-30) REVERT: E 218 ASP cc_start: 0.8808 (t0) cc_final: 0.8269 (t0) REVERT: E 244 LYS cc_start: 0.9486 (OUTLIER) cc_final: 0.9127 (ttmm) REVERT: E 319 GLN cc_start: 0.8920 (tp40) cc_final: 0.8698 (tp40) REVERT: E 341 GLU cc_start: 0.8581 (mp0) cc_final: 0.8076 (mp0) REVERT: E 366 ILE cc_start: 0.9533 (mm) cc_final: 0.9116 (tp) REVERT: E 395 ASP cc_start: 0.9117 (t70) cc_final: 0.8844 (t70) REVERT: E 397 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: E 439 ARG cc_start: 0.1618 (mmm160) cc_final: 0.1230 (ttt180) REVERT: F 122 ASN cc_start: 0.9221 (m110) cc_final: 0.8991 (m-40) REVERT: F 195 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8931 (mmtm) REVERT: F 215 THR cc_start: 0.8526 (m) cc_final: 0.8183 (p) REVERT: F 217 MET cc_start: 0.8134 (tpp) cc_final: 0.7749 (tpp) REVERT: F 231 ARG cc_start: 0.8538 (mmm160) cc_final: 0.8174 (mmm160) REVERT: F 305 ASP cc_start: 0.9118 (m-30) cc_final: 0.8462 (t70) REVERT: F 343 SER cc_start: 0.9048 (t) cc_final: 0.8412 (p) REVERT: T 110 MET cc_start: 0.4076 (mpp) cc_final: 0.3655 (mpp) outliers start: 86 outliers final: 73 residues processed: 356 average time/residue: 0.1477 time to fit residues: 83.9123 Evaluate side-chains 361 residues out of total 2397 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 280 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 287 PHE Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 328 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 372 CYS Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 328 CYS Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 311 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 396 CYS Chi-restraints excluded: chain D residue 400 TYR Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 102 ASP Chi-restraints excluded: chain S residue 109 HIS Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 244 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 328 CYS Chi-restraints excluded: chain E residue 339 LEU Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 430 CYS Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 324 GLU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 355 ILE Chi-restraints excluded: chain F residue 372 CYS Chi-restraints excluded: chain F residue 400 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1741 > 50: distance: 13 - 96: 27.764 distance: 45 - 50: 15.180 distance: 50 - 51: 7.858 distance: 51 - 52: 16.215 distance: 51 - 54: 9.981 distance: 52 - 53: 24.887 distance: 52 - 56: 12.621 distance: 54 - 55: 29.620 distance: 55 - 148: 15.866 distance: 56 - 57: 36.341 distance: 57 - 58: 36.073 distance: 57 - 60: 29.597 distance: 58 - 59: 10.103 distance: 58 - 64: 36.378 distance: 60 - 61: 16.163 distance: 61 - 62: 32.050 distance: 61 - 63: 21.436 distance: 64 - 65: 19.996 distance: 65 - 66: 37.726 distance: 66 - 67: 10.973 distance: 66 - 68: 35.470 distance: 68 - 69: 44.899 distance: 69 - 70: 36.304 distance: 69 - 72: 26.359 distance: 70 - 71: 25.753 distance: 70 - 76: 34.107 distance: 72 - 73: 29.227 distance: 73 - 74: 27.371 distance: 73 - 75: 24.589 distance: 76 - 77: 15.975 distance: 76 - 82: 10.102 distance: 77 - 78: 48.039 distance: 77 - 80: 9.597 distance: 78 - 79: 47.635 distance: 78 - 83: 12.275 distance: 80 - 81: 23.035 distance: 81 - 82: 11.768 distance: 83 - 84: 5.455 distance: 84 - 85: 49.588 distance: 84 - 87: 39.767 distance: 85 - 86: 30.798 distance: 85 - 91: 41.067 distance: 87 - 88: 37.692 distance: 88 - 89: 36.941 distance: 88 - 90: 37.459 distance: 91 - 92: 10.654 distance: 92 - 93: 11.743 distance: 92 - 95: 19.594 distance: 93 - 94: 13.973 distance: 93 - 97: 7.866 distance: 95 - 96: 34.577 distance: 97 - 98: 12.445 distance: 98 - 99: 24.528 distance: 98 - 101: 18.087 distance: 99 - 106: 26.710 distance: 101 - 102: 27.185 distance: 102 - 103: 11.610 distance: 103 - 104: 11.898 distance: 103 - 105: 6.505 distance: 106 - 107: 16.513 distance: 107 - 108: 9.132 distance: 107 - 110: 24.482 distance: 108 - 109: 5.010 distance: 108 - 114: 29.359 distance: 110 - 111: 9.203 distance: 111 - 112: 11.008 distance: 111 - 113: 20.665 distance: 114 - 115: 13.530 distance: 115 - 116: 14.060 distance: 116 - 117: 12.541 distance: 116 - 118: 15.722 distance: 117 - 132: 23.604