Starting phenix.real_space_refine on Sat Aug 23 07:30:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2m_38017/08_2025/8x2m_38017_neut.cif" } resolution = 3.31 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 105 5.16 5 C 6720 2.51 5 N 1788 2.21 5 O 1932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10545 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4710 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 28, 'TRANS': 552} Chain breaks: 11 Chain: "B" Number of atoms: 4614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4614 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 28, 'TRANS': 541} Chain breaks: 11 Chain: "C" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 355 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain breaks: 2 Chain: "D" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 253 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 1 Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 359 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain breaks: 1 Chain: "F" Number of atoms: 254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 254 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain breaks: 3 Time building chain proxies: 2.83, per 1000 atoms: 0.27 Number of scatterers: 10545 At special positions: 0 Unit cell: (144.54, 103.62, 83.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 105 16.00 O 1932 8.00 N 1788 7.00 C 6720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 8 " - pdb=" SG CYS B 26 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 188 " distance=2.03 Simple disulfide: pdb=" SG CYS B 192 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 207 " distance=2.03 Simple disulfide: pdb=" SG CYS B 208 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 259 " - pdb=" SG CYS B 284 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 435 " - pdb=" SG CYS B 468 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 61 " 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: 0.81 Conformation dependent library (CDL) restraints added in 356.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 23 sheets defined 21.8% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 removed outlier: 3.689A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS A 21 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.532A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 257 through 268 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.619A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.516A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.512A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 714 removed outlier: 3.549A pdb=" N GLU A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 24 removed outlier: 3.616A pdb=" N GLU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 Processing helix chain 'B' and resid 132 through 136 removed outlier: 3.727A pdb=" N ARG B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.745A pdb=" N ASP B 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN B 152 " --> pdb=" O LYS B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 152' Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.871A pdb=" N CYS B 259 " --> pdb=" O ASN B 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.755A pdb=" N GLU B 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 329 Processing helix chain 'B' and resid 350 through 359 Processing helix chain 'B' and resid 435 through 447 removed outlier: 3.508A pdb=" N MET B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 498 No H-bonds generated for 'chain 'B' and resid 496 through 498' Processing helix chain 'B' and resid 693 through 714 removed outlier: 3.517A pdb=" N GLU B 697 " --> pdb=" O LEU B 693 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 53 through 58 Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'D' and resid 8 through 12 Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 53 through 58 Processing helix chain 'E' and resid 7 through 19 removed outlier: 3.823A pdb=" N VAL E 11 " --> pdb=" O GLY E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 48 removed outlier: 3.536A pdb=" N GLU E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.776A pdb=" N TYR E 60 " --> pdb=" O LEU E 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 19 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 53 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 removed outlier: 5.775A pdb=" N GLU A 6 " --> pdb=" O CYS A 26 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.221A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ARG A 118 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A 94 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 120 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE A 96 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 removed outlier: 3.850A pdb=" N VAL A 179 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.088A pdb=" N ALA A 227 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ASN A 215 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N CYS A 225 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 253 removed outlier: 6.409A pdb=" N HIS A 247 " --> pdb=" O CYS A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.657A pdb=" N THR A 302 " --> pdb=" O THR A 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 313 through 321 removed outlier: 5.409A pdb=" N HIS A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN A 337 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS A 369 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 340 " --> pdb=" O LYS A 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 313 through 321 removed outlier: 5.409A pdb=" N HIS A 313 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ASN A 337 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 315 " --> pdb=" O ASN A 337 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N SER A 339 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY A 317 " --> pdb=" O SER A 339 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE A 341 " --> pdb=" O GLY A 317 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A 319 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 336 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE A 364 " --> pdb=" O ARG A 389 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 398 through 400 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 removed outlier: 6.462A pdb=" N GLU A 471 " --> pdb=" O LYS A 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 475 through 480 Processing sheet with id=AB3, first strand: chain 'A' and resid 530 through 534 removed outlier: 4.017A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 532 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 8 removed outlier: 5.559A pdb=" N GLU B 6 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.152A pdb=" N MET B 11 " --> pdb=" O GLN B 34 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N LEU B 36 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B 33 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE B 64 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 35 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL B 66 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 37 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B 61 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE B 96 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 63 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 93 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLU B 120 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE B 95 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 117 " --> pdb=" O TYR B 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'B' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'B' and resid 246 through 247 Processing sheet with id=AB8, first strand: chain 'B' and resid 278 through 280 Processing sheet with id=AB9, first strand: chain 'B' and resid 292 through 295 removed outlier: 4.849A pdb=" N ASN B 295 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU B 300 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 320 through 321 removed outlier: 7.450A pdb=" N LEU B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N LEU B 403 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 370 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 336 Processing sheet with id=AC3, first strand: chain 'B' and resid 471 through 472 removed outlier: 6.464A pdb=" N GLU B 471 " --> pdb=" O LYS B 582 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 475 through 480 Processing sheet with id=AC5, first strand: chain 'B' and resid 530 through 531 removed outlier: 3.633A pdb=" N TYR B 507 " --> pdb=" O THR B 530 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 502 " --> pdb=" O LEU B 569 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 569 " --> pdb=" O GLY B 502 " (cutoff:3.500A) 203 hydrogen bonds defined for protein. 510 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: 1.28 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3409 1.35 - 1.46: 2571 1.46 - 1.58: 4666 1.58 - 1.70: 0 1.70 - 1.82: 127 Bond restraints: 10773 Sorted by residual: bond pdb=" C LEU B 556 " pdb=" N LYS B 557 " ideal model delta sigma weight residual 1.331 1.369 -0.038 2.07e-02 2.33e+03 3.29e+00 bond pdb=" CA ILE A 388 " pdb=" CB ILE A 388 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 9.37e-01 bond pdb=" CA VAL A 191 " pdb=" CB VAL A 191 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.43e-01 bond pdb=" CB PHE E 16 " pdb=" CG PHE E 16 " ideal model delta sigma weight residual 1.502 1.523 -0.021 2.30e-02 1.89e+03 8.12e-01 bond pdb=" SD MET A 38 " pdb=" CE MET A 38 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 8.03e-01 ... (remaining 10768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 14287 2.00 - 3.99: 223 3.99 - 5.99: 25 5.99 - 7.98: 5 7.98 - 9.98: 5 Bond angle restraints: 14545 Sorted by residual: angle pdb=" CB MET A 110 " pdb=" CG MET A 110 " pdb=" SD MET A 110 " ideal model delta sigma weight residual 112.70 122.68 -9.98 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " ideal model delta sigma weight residual 112.70 121.71 -9.01 3.00e+00 1.11e-01 9.02e+00 angle pdb=" CB MET B 294 " pdb=" CG MET B 294 " pdb=" SD MET B 294 " ideal model delta sigma weight residual 112.70 121.09 -8.39 3.00e+00 1.11e-01 7.82e+00 angle pdb=" N VAL A 226 " pdb=" CA VAL A 226 " pdb=" C VAL A 226 " ideal model delta sigma weight residual 111.67 109.02 2.65 9.50e-01 1.11e+00 7.79e+00 angle pdb=" CA LEU A 233 " pdb=" CB LEU A 233 " pdb=" CG LEU A 233 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 ... (remaining 14540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5610 17.93 - 35.86: 675 35.86 - 53.79: 184 53.79 - 71.72: 23 71.72 - 89.65: 14 Dihedral angle restraints: 6506 sinusoidal: 2719 harmonic: 3787 Sorted by residual: dihedral pdb=" CB CYS A 259 " pdb=" SG CYS A 259 " pdb=" SG CYS A 284 " pdb=" CB CYS A 284 " ideal model delta sinusoidal sigma weight residual -86.00 -172.17 86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CB CYS A 8 " pdb=" SG CYS A 8 " pdb=" SG CYS A 26 " pdb=" CB CYS A 26 " ideal model delta sinusoidal sigma weight residual 93.00 173.18 -80.18 1 1.00e+01 1.00e-02 7.96e+01 dihedral pdb=" CB CYS B 8 " pdb=" SG CYS B 8 " pdb=" SG CYS B 26 " pdb=" CB CYS B 26 " ideal model delta sinusoidal sigma weight residual 93.00 160.07 -67.07 1 1.00e+01 1.00e-02 5.86e+01 ... (remaining 6503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 931 0.030 - 0.060: 416 0.060 - 0.090: 139 0.090 - 0.120: 70 0.120 - 0.150: 33 Chirality restraints: 1589 Sorted by residual: chirality pdb=" CA PRO B 43 " pdb=" N PRO B 43 " pdb=" C PRO B 43 " pdb=" CB PRO B 43 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE B 145 " pdb=" N ILE B 145 " pdb=" C ILE B 145 " pdb=" CB ILE B 145 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA ILE B 112 " pdb=" N ILE B 112 " pdb=" C ILE B 112 " pdb=" CB ILE B 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1586 not shown) Planarity restraints: 1859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 494 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.62e+00 pdb=" N PRO A 495 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 495 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 495 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 557 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO B 558 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 558 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 558 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 234 " -0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" CG ASP B 234 " 0.030 2.00e-02 2.50e+03 pdb=" OD1 ASP B 234 " -0.011 2.00e-02 2.50e+03 pdb=" OD2 ASP B 234 " -0.010 2.00e-02 2.50e+03 ... (remaining 1856 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 214 2.69 - 3.24: 9953 3.24 - 3.79: 15738 3.79 - 4.35: 21227 4.35 - 4.90: 34694 Nonbonded interactions: 81826 Sorted by model distance: nonbonded pdb=" OG1 THR B 130 " pdb=" O CYS B 182 " model vdw 2.137 3.040 nonbonded pdb=" OG1 THR A 130 " pdb=" O CYS A 182 " model vdw 2.156 3.040 nonbonded pdb=" OE1 GLU B 353 " pdb=" ND2 ASN B 357 " model vdw 2.221 3.120 nonbonded pdb=" OG1 THR B 41 " pdb=" O TYR B 67 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 3 " pdb=" O VAL A 226 " model vdw 2.251 3.040 ... (remaining 81821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 13 or resid 15 through 160 or resid 169 through \ 249 or resid 252 through 267 or resid 274 through 452 or resid 456 through 514 o \ r resid 528 through 540 or resid 546 through 572 or resid 579 through 717)) selection = (chain 'B' and (resid 3 through 196 or resid 198 through 717)) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 4 through 6 or resid 8 through 63)) } ncs_group { reference = (chain 'D' and (resid 7 through 9 or resid 11 through 61 or resid 63)) selection = (chain 'F' and (resid 7 through 25 or resid 51 through 63)) } 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: 12.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10802 Z= 0.128 Angle : 0.629 9.979 14603 Z= 0.319 Chirality : 0.044 0.150 1589 Planarity : 0.004 0.054 1859 Dihedral : 16.670 89.647 3961 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.51 % Allowed : 24.28 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.23), residues: 1238 helix: -0.86 (0.35), residues: 225 sheet: -1.44 (0.43), residues: 138 loop : -1.43 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 83 TYR 0.022 0.001 TYR B 401 PHE 0.016 0.001 PHE B 64 TRP 0.026 0.002 TRP A 414 HIS 0.005 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00283 (10773) covalent geometry : angle 0.62692 (14545) SS BOND : bond 0.00245 ( 29) SS BOND : angle 1.06062 ( 58) hydrogen bonds : bond 0.26430 ( 203) hydrogen bonds : angle 8.56485 ( 510) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 247 average time/residue: 0.1161 time to fit residues: 37.6366 Evaluate side-chains 124 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 280 HIS A 407 ASN A 417 HIS ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.087388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.068061 restraints weight = 38588.788| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 4.43 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10802 Z= 0.155 Angle : 0.705 8.857 14603 Z= 0.358 Chirality : 0.047 0.168 1589 Planarity : 0.005 0.056 1859 Dihedral : 5.189 24.771 1402 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.72 % Allowed : 22.43 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.23), residues: 1238 helix: -0.31 (0.37), residues: 213 sheet: -1.70 (0.41), residues: 150 loop : -1.35 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 50 TYR 0.024 0.002 TYR B 144 PHE 0.014 0.001 PHE A 258 TRP 0.014 0.001 TRP A 414 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00356 (10773) covalent geometry : angle 0.70340 (14545) SS BOND : bond 0.00333 ( 29) SS BOND : angle 1.06846 ( 58) hydrogen bonds : bond 0.05411 ( 203) hydrogen bonds : angle 6.83671 ( 510) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 120 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7712 (mtp85) REVERT: A 36 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 47 ARG cc_start: 0.8589 (tpp-160) cc_final: 0.8378 (tpp-160) REVERT: A 131 ILE cc_start: 0.6065 (mm) cc_final: 0.5770 (mm) REVERT: A 430 TYR cc_start: 0.7911 (m-80) cc_final: 0.7263 (m-80) REVERT: B 358 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8872 (pp) REVERT: B 430 TYR cc_start: 0.7522 (t80) cc_final: 0.7217 (t80) REVERT: B 459 LEU cc_start: 0.8604 (mm) cc_final: 0.8341 (mm) REVERT: B 474 LYS cc_start: 0.8991 (mttp) cc_final: 0.8717 (mtmm) REVERT: B 695 GLU cc_start: 0.8838 (pt0) cc_final: 0.8559 (tm-30) REVERT: C 59 MET cc_start: 0.7988 (ptm) cc_final: 0.7704 (ptt) REVERT: D 15 GLN cc_start: 0.9495 (pt0) cc_final: 0.9267 (mp10) REVERT: E 46 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8248 (mt-10) REVERT: E 55 ARG cc_start: 0.9157 (tpm170) cc_final: 0.8954 (tmm-80) outliers start: 56 outliers final: 22 residues processed: 166 average time/residue: 0.1124 time to fit residues: 25.0717 Evaluate side-chains 126 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 512 TYR Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain D residue 61 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.085089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.065278 restraints weight = 38731.551| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.42 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10802 Z= 0.217 Angle : 0.698 8.270 14603 Z= 0.355 Chirality : 0.046 0.155 1589 Planarity : 0.005 0.063 1859 Dihedral : 5.311 27.230 1402 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.89 % Allowed : 22.26 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.23), residues: 1238 helix: -0.22 (0.37), residues: 220 sheet: -1.86 (0.40), residues: 143 loop : -1.37 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 50 TYR 0.022 0.002 TYR A 430 PHE 0.022 0.002 PHE C 16 TRP 0.018 0.002 TRP A 412 HIS 0.011 0.001 HIS A 417 Details of bonding type rmsd covalent geometry : bond 0.00506 (10773) covalent geometry : angle 0.69579 (14545) SS BOND : bond 0.00366 ( 29) SS BOND : angle 1.09579 ( 58) hydrogen bonds : bond 0.04661 ( 203) hydrogen bonds : angle 6.49419 ( 510) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 105 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7651 (mtp85) REVERT: A 108 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7331 (m-40) REVERT: A 429 HIS cc_start: 0.8404 (OUTLIER) cc_final: 0.7891 (t-90) REVERT: B 358 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8936 (pp) REVERT: B 430 TYR cc_start: 0.7657 (t80) cc_final: 0.7388 (t80) REVERT: B 474 LYS cc_start: 0.9044 (mttp) cc_final: 0.8735 (mtmm) REVERT: B 554 ARG cc_start: 0.8408 (mpp80) cc_final: 0.8108 (mpp80) REVERT: B 695 GLU cc_start: 0.8847 (pt0) cc_final: 0.8595 (tm-30) REVERT: C 55 ARG cc_start: 0.8712 (tpm170) cc_final: 0.8412 (tpm170) outliers start: 58 outliers final: 31 residues processed: 155 average time/residue: 0.1075 time to fit residues: 23.0151 Evaluate side-chains 131 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain E residue 48 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 123 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 0.6980 chunk 127 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 417 HIS A 429 HIS A 546 GLN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.086210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.066517 restraints weight = 38903.286| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 4.45 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10802 Z= 0.122 Angle : 0.635 8.586 14603 Z= 0.321 Chirality : 0.045 0.161 1589 Planarity : 0.004 0.055 1859 Dihedral : 5.082 26.474 1402 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.55 % Allowed : 23.19 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1238 helix: -0.04 (0.38), residues: 215 sheet: -1.60 (0.41), residues: 150 loop : -1.23 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 50 TYR 0.012 0.001 TYR A 60 PHE 0.021 0.001 PHE A 258 TRP 0.017 0.001 TRP B 412 HIS 0.004 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00281 (10773) covalent geometry : angle 0.63344 (14545) SS BOND : bond 0.00259 ( 29) SS BOND : angle 0.89777 ( 58) hydrogen bonds : bond 0.03972 ( 203) hydrogen bonds : angle 6.35204 ( 510) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 105 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 HIS cc_start: 0.8448 (OUTLIER) cc_final: 0.8109 (t-170) REVERT: B 47 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8078 (mmp-170) REVERT: B 69 LEU cc_start: 0.8823 (tp) cc_final: 0.8484 (tp) REVERT: B 81 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 314 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 358 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8895 (pp) REVERT: B 430 TYR cc_start: 0.7568 (t80) cc_final: 0.7200 (t80) REVERT: B 474 LYS cc_start: 0.9019 (mttp) cc_final: 0.8724 (mtmm) REVERT: B 501 LEU cc_start: 0.9550 (mt) cc_final: 0.9121 (mp) REVERT: B 554 ARG cc_start: 0.8271 (mpp80) cc_final: 0.7963 (mpp80) REVERT: B 569 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8742 (pt) REVERT: B 695 GLU cc_start: 0.8819 (pt0) cc_final: 0.8501 (tm-30) REVERT: C 55 ARG cc_start: 0.8717 (tpm170) cc_final: 0.8478 (tpm170) REVERT: C 59 MET cc_start: 0.8027 (ptm) cc_final: 0.7821 (ptt) REVERT: E 56 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8000 (ptm-80) outliers start: 54 outliers final: 28 residues processed: 148 average time/residue: 0.1148 time to fit residues: 23.6254 Evaluate side-chains 127 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 429 HIS Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 56 ARG Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 57 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.084937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.065060 restraints weight = 38465.826| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.40 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10802 Z= 0.168 Angle : 0.648 9.912 14603 Z= 0.328 Chirality : 0.045 0.174 1589 Planarity : 0.004 0.054 1859 Dihedral : 5.104 27.304 1402 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.89 % Allowed : 24.11 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.23), residues: 1238 helix: -0.10 (0.38), residues: 212 sheet: -1.63 (0.42), residues: 148 loop : -1.25 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 50 TYR 0.013 0.001 TYR B 507 PHE 0.035 0.002 PHE A 258 TRP 0.022 0.001 TRP B 412 HIS 0.012 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00395 (10773) covalent geometry : angle 0.64714 (14545) SS BOND : bond 0.00335 ( 29) SS BOND : angle 0.90539 ( 58) hydrogen bonds : bond 0.03860 ( 203) hydrogen bonds : angle 6.27527 ( 510) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 95 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 19 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7828 (mmm-85) REVERT: A 47 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8488 (tpp-160) REVERT: B 47 ARG cc_start: 0.8487 (mmm160) cc_final: 0.8099 (mmp-170) REVERT: B 69 LEU cc_start: 0.8854 (tp) cc_final: 0.8455 (tp) REVERT: B 358 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8901 (pp) REVERT: B 474 LYS cc_start: 0.9040 (mttp) cc_final: 0.8740 (mtmm) REVERT: B 504 MET cc_start: 0.8488 (mmm) cc_final: 0.8253 (mmm) REVERT: B 554 ARG cc_start: 0.8577 (mpp80) cc_final: 0.8235 (mpp80) REVERT: B 695 GLU cc_start: 0.8804 (pt0) cc_final: 0.8484 (tm-30) REVERT: C 55 ARG cc_start: 0.8734 (tpm170) cc_final: 0.8460 (tpm170) REVERT: E 46 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8325 (tt0) REVERT: E 53 ASP cc_start: 0.8487 (p0) cc_final: 0.8242 (p0) REVERT: E 55 ARG cc_start: 0.9135 (tpm170) cc_final: 0.8645 (tpm170) outliers start: 58 outliers final: 37 residues processed: 143 average time/residue: 0.1152 time to fit residues: 22.9262 Evaluate side-chains 130 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain E residue 14 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 691 GLN C 26 ASN ** F 15 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.085026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.065082 restraints weight = 38829.249| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.43 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10802 Z= 0.155 Angle : 0.635 9.405 14603 Z= 0.318 Chirality : 0.045 0.157 1589 Planarity : 0.004 0.054 1859 Dihedral : 5.043 26.216 1402 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.55 % Allowed : 24.20 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.23), residues: 1238 helix: -0.07 (0.38), residues: 214 sheet: -1.66 (0.42), residues: 146 loop : -1.22 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 50 TYR 0.012 0.001 TYR A 60 PHE 0.031 0.001 PHE A 258 TRP 0.020 0.001 TRP B 412 HIS 0.008 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00367 (10773) covalent geometry : angle 0.63406 (14545) SS BOND : bond 0.00305 ( 29) SS BOND : angle 0.83510 ( 58) hydrogen bonds : bond 0.03586 ( 203) hydrogen bonds : angle 6.13820 ( 510) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 0.375 Fit side-chains REVERT: A 19 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7743 (mmm-85) REVERT: A 47 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8481 (tpp-160) REVERT: A 430 TYR cc_start: 0.7985 (m-80) cc_final: 0.7552 (m-80) REVERT: B 47 ARG cc_start: 0.8496 (mmm160) cc_final: 0.8122 (mmp-170) REVERT: B 56 MET cc_start: 0.9026 (ttt) cc_final: 0.8769 (ttt) REVERT: B 69 LEU cc_start: 0.8864 (tp) cc_final: 0.8513 (tp) REVERT: B 81 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8214 (m) REVERT: B 358 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8878 (pp) REVERT: B 504 MET cc_start: 0.8495 (mmm) cc_final: 0.8269 (mmm) REVERT: B 554 ARG cc_start: 0.8515 (mpp80) cc_final: 0.8185 (mpp80) REVERT: B 695 GLU cc_start: 0.8809 (pt0) cc_final: 0.8449 (tm-30) REVERT: C 55 ARG cc_start: 0.8738 (tpm170) cc_final: 0.8452 (tpm170) REVERT: E 53 ASP cc_start: 0.8583 (p0) cc_final: 0.8234 (p0) REVERT: F 24 TYR cc_start: 0.8520 (p90) cc_final: 0.8295 (p90) outliers start: 54 outliers final: 38 residues processed: 140 average time/residue: 0.1189 time to fit residues: 22.6126 Evaluate side-chains 130 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 ASN B 691 GLN C 26 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.083276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.063278 restraints weight = 38968.486| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 4.33 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10802 Z= 0.254 Angle : 0.715 10.437 14603 Z= 0.359 Chirality : 0.047 0.170 1589 Planarity : 0.005 0.055 1859 Dihedral : 5.349 29.676 1402 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.89 % Allowed : 24.45 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.23), residues: 1238 helix: -0.31 (0.37), residues: 213 sheet: -1.64 (0.42), residues: 145 loop : -1.29 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 56 TYR 0.015 0.002 TYR B 367 PHE 0.031 0.002 PHE A 258 TRP 0.013 0.002 TRP B 412 HIS 0.005 0.001 HIS A 100 Details of bonding type rmsd covalent geometry : bond 0.00594 (10773) covalent geometry : angle 0.71271 (14545) SS BOND : bond 0.00424 ( 29) SS BOND : angle 1.17432 ( 58) hydrogen bonds : bond 0.03945 ( 203) hydrogen bonds : angle 6.23406 ( 510) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 87 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8760 (tpp-160) cc_final: 0.8485 (tpp-160) REVERT: A 430 TYR cc_start: 0.8191 (m-80) cc_final: 0.7799 (m-80) REVERT: B 81 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 504 MET cc_start: 0.8561 (mmm) cc_final: 0.8314 (mmt) REVERT: B 554 ARG cc_start: 0.8615 (mpp80) cc_final: 0.8242 (mpp80) REVERT: C 55 ARG cc_start: 0.8810 (tpm170) cc_final: 0.8533 (tpm170) REVERT: D 61 CYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8117 (t) REVERT: E 46 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8173 (tt0) REVERT: E 53 ASP cc_start: 0.8521 (p0) cc_final: 0.8200 (p0) outliers start: 58 outliers final: 39 residues processed: 135 average time/residue: 0.1127 time to fit residues: 21.0884 Evaluate side-chains 124 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 83 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 61 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.084421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064459 restraints weight = 38612.391| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 4.38 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10802 Z= 0.152 Angle : 0.673 11.021 14603 Z= 0.330 Chirality : 0.045 0.154 1589 Planarity : 0.004 0.054 1859 Dihedral : 5.138 26.950 1402 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.05 % Allowed : 25.63 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.24), residues: 1238 helix: -0.01 (0.38), residues: 211 sheet: -1.59 (0.43), residues: 143 loop : -1.19 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 50 TYR 0.012 0.001 TYR A 60 PHE 0.026 0.001 PHE A 258 TRP 0.019 0.002 TRP B 412 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00359 (10773) covalent geometry : angle 0.67122 (14545) SS BOND : bond 0.00297 ( 29) SS BOND : angle 0.99133 ( 58) hydrogen bonds : bond 0.03566 ( 203) hydrogen bonds : angle 6.06914 ( 510) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 93 time to evaluate : 0.471 Fit side-chains REVERT: A 47 ARG cc_start: 0.8762 (tpp-160) cc_final: 0.8484 (tpp-160) REVERT: A 430 TYR cc_start: 0.8140 (m-80) cc_final: 0.7765 (m-80) REVERT: B 47 ARG cc_start: 0.8519 (mmm160) cc_final: 0.8316 (mmm160) REVERT: B 56 MET cc_start: 0.9028 (ttt) cc_final: 0.8765 (ttt) REVERT: B 504 MET cc_start: 0.8503 (mmm) cc_final: 0.8280 (mmt) REVERT: B 553 MET cc_start: 0.8480 (tpp) cc_final: 0.8095 (tpt) REVERT: B 554 ARG cc_start: 0.8601 (mpp80) cc_final: 0.8202 (mpp80) REVERT: C 55 ARG cc_start: 0.8815 (tpm170) cc_final: 0.8541 (tpm170) outliers start: 48 outliers final: 39 residues processed: 132 average time/residue: 0.1241 time to fit residues: 22.3493 Evaluate side-chains 126 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 87 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 54 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 109 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.082436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.062404 restraints weight = 38743.769| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 4.31 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10802 Z= 0.261 Angle : 0.761 11.759 14603 Z= 0.380 Chirality : 0.048 0.176 1589 Planarity : 0.005 0.056 1859 Dihedral : 5.459 28.390 1402 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 4.05 % Allowed : 25.63 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.23), residues: 1238 helix: -0.23 (0.36), residues: 213 sheet: -1.78 (0.42), residues: 145 loop : -1.41 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 50 TYR 0.016 0.002 TYR B 367 PHE 0.029 0.002 PHE A 258 TRP 0.012 0.002 TRP B 133 HIS 0.005 0.001 HIS B 417 Details of bonding type rmsd covalent geometry : bond 0.00607 (10773) covalent geometry : angle 0.75865 (14545) SS BOND : bond 0.00448 ( 29) SS BOND : angle 1.22411 ( 58) hydrogen bonds : bond 0.03962 ( 203) hydrogen bonds : angle 6.22177 ( 510) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 87 time to evaluate : 0.446 Fit side-chains REVERT: A 47 ARG cc_start: 0.8778 (tpp-160) cc_final: 0.8320 (tpp-160) REVERT: A 430 TYR cc_start: 0.8270 (m-80) cc_final: 0.7845 (m-80) REVERT: B 56 MET cc_start: 0.9069 (ttt) cc_final: 0.8814 (ttt) REVERT: B 504 MET cc_start: 0.8583 (mmm) cc_final: 0.8318 (mmt) REVERT: B 554 ARG cc_start: 0.8629 (mpp80) cc_final: 0.8221 (mpp80) REVERT: C 55 ARG cc_start: 0.8876 (tpm170) cc_final: 0.8598 (tpm170) REVERT: C 56 ARG cc_start: 0.8183 (ptt-90) cc_final: 0.7964 (ttp-170) outliers start: 48 outliers final: 44 residues processed: 127 average time/residue: 0.1250 time to fit residues: 21.9127 Evaluate side-chains 131 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 87 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 29 optimal weight: 0.0770 chunk 5 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN F 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.084818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.064949 restraints weight = 38002.342| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 4.39 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10802 Z= 0.115 Angle : 0.704 12.750 14603 Z= 0.340 Chirality : 0.045 0.181 1589 Planarity : 0.004 0.057 1859 Dihedral : 5.083 25.835 1402 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.95 % Allowed : 26.81 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.23), residues: 1238 helix: -0.19 (0.37), residues: 221 sheet: -1.49 (0.45), residues: 128 loop : -1.33 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 50 TYR 0.012 0.001 TYR A 60 PHE 0.029 0.001 PHE E 16 TRP 0.026 0.002 TRP B 412 HIS 0.002 0.000 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00268 (10773) covalent geometry : angle 0.70379 (14545) SS BOND : bond 0.00243 ( 29) SS BOND : angle 0.85282 ( 58) hydrogen bonds : bond 0.03555 ( 203) hydrogen bonds : angle 6.01423 ( 510) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2476 Ramachandran restraints generated. 1238 Oldfield, 0 Emsley, 1238 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.327 Fit side-chains REVERT: A 47 ARG cc_start: 0.8759 (tpp-160) cc_final: 0.8307 (tpp-160) REVERT: A 430 TYR cc_start: 0.8107 (m-80) cc_final: 0.7675 (m-80) REVERT: B 47 ARG cc_start: 0.8511 (mmm160) cc_final: 0.8058 (mmp-170) REVERT: B 504 MET cc_start: 0.8480 (mmm) cc_final: 0.8253 (mmt) REVERT: B 554 ARG cc_start: 0.8554 (mpp80) cc_final: 0.8201 (mpp80) REVERT: C 55 ARG cc_start: 0.8864 (tpm170) cc_final: 0.8597 (tpm170) outliers start: 35 outliers final: 34 residues processed: 122 average time/residue: 0.1346 time to fit residues: 22.1622 Evaluate side-chains 122 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 15 ASN Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 288 CYS Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 417 HIS Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 CYS Chi-restraints excluded: chain B residue 259 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 548 HIS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN A 561 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.084356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.064515 restraints weight = 38748.885| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.38 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10802 Z= 0.139 Angle : 0.700 11.585 14603 Z= 0.338 Chirality : 0.045 0.223 1589 Planarity : 0.004 0.055 1859 Dihedral : 5.033 25.918 1402 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.95 % Allowed : 27.23 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.24), residues: 1238 helix: 0.08 (0.38), residues: 210 sheet: -1.52 (0.43), residues: 143 loop : -1.19 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 50 TYR 0.021 0.001 TYR B 507 PHE 0.026 0.001 PHE E 16 TRP 0.018 0.001 TRP B 412 HIS 0.003 0.001 HIS A 247 Details of bonding type rmsd covalent geometry : bond 0.00331 (10773) covalent geometry : angle 0.69923 (14545) SS BOND : bond 0.00270 ( 29) SS BOND : angle 0.86378 ( 58) hydrogen bonds : bond 0.03484 ( 203) hydrogen bonds : angle 5.98753 ( 510) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2252.38 seconds wall clock time: 39 minutes 39.96 seconds (2379.96 seconds total)