Starting phenix.real_space_refine on Sun Dec 29 12:57:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2m_38017/12_2024/8x2m_38017_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2m_38017/12_2024/8x2m_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_38017/12_2024/8x2m_38017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2m_38017/12_2024/8x2m_38017.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2m_38017/12_2024/8x2m_38017_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2m_38017/12_2024/8x2m_38017_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 2.28, per 1000 atoms: 0.22 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.40 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: 3.79 Time building geometry restraints manager: 2.94 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: 42.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.190 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.110 ------------------------------------------------------------------------------- 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 10773 Z= 0.181 Angle : 0.627 9.979 14545 Z= 0.318 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.002 TRP A 414 HIS 0.005 0.001 HIS A 247 PHE 0.016 0.001 PHE B 64 TYR 0.022 0.001 TYR B 401 ARG 0.003 0.000 ARG B 83 *********************** 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 : 1.202 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: 0.3013 time to fit residues: 97.6284 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 : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 280 HIS A 407 ASN A 417 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 275 HIS B 691 GLN C 26 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 10773 Z= 0.439 Angle : 0.785 9.328 14545 Z= 0.403 Chirality : 0.050 0.181 1589 Planarity : 0.005 0.058 1859 Dihedral : 5.504 26.023 1402 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 5.56 % Allowed : 22.93 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.23), residues: 1238 helix: -0.43 (0.36), residues: 214 sheet: -1.93 (0.39), residues: 148 loop : -1.46 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 414 HIS 0.007 0.002 HIS A 417 PHE 0.017 0.002 PHE B 64 TYR 0.021 0.002 TYR B 367 ARG 0.014 0.001 ARG E 50 *********************** 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 183 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 117 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 TYR cc_start: 0.6856 (m-80) cc_final: 0.6602 (m-80) outliers start: 66 outliers final: 32 residues processed: 172 average time/residue: 0.2794 time to fit residues: 64.8639 Evaluate side-chains 133 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 57 ILE 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 518 PHE Chi-restraints excluded: chain A residue 534 ILE 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 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 449 LYS Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 579 TYR Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain F residue 54 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 126 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10773 Z= 0.192 Angle : 0.670 9.563 14545 Z= 0.338 Chirality : 0.045 0.156 1589 Planarity : 0.004 0.055 1859 Dihedral : 5.215 26.929 1402 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.79 % Allowed : 22.60 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1238 helix: -0.09 (0.38), residues: 213 sheet: -1.74 (0.40), residues: 150 loop : -1.32 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 412 HIS 0.006 0.001 HIS A 417 PHE 0.024 0.001 PHE C 16 TYR 0.019 0.001 TYR A 430 ARG 0.008 0.000 ARG E 50 *********************** 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 151 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7892 (mp) REVERT: B 294 MET cc_start: 0.7018 (tpp) cc_final: 0.6646 (tpp) outliers start: 45 outliers final: 24 residues processed: 144 average time/residue: 0.2558 time to fit residues: 51.7900 Evaluate side-chains 121 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 122 ASN Chi-restraints excluded: chain A residue 178 PHE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 554 ARG Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 692 ILE 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 259 CYS 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 24 TYR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 56 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS A 417 HIS A 513 GLN ** B 143 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10773 Z= 0.321 Angle : 0.683 8.848 14545 Z= 0.348 Chirality : 0.046 0.148 1589 Planarity : 0.004 0.056 1859 Dihedral : 5.278 28.030 1402 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.81 % Allowed : 22.77 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.23), residues: 1238 helix: -0.15 (0.37), residues: 215 sheet: -1.84 (0.39), residues: 155 loop : -1.33 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 412 HIS 0.006 0.001 HIS A 429 PHE 0.022 0.002 PHE A 258 TYR 0.015 0.002 TYR A 430 ARG 0.014 0.001 ARG E 55 *********************** 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: 57 poor density : 102 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 692 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8087 (mp) outliers start: 57 outliers final: 33 residues processed: 147 average time/residue: 0.2675 time to fit residues: 54.2853 Evaluate side-chains 128 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 1.352 ------------------------------------------------------------------------------- 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 109 LEU 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 226 VAL Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 315 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 A residue 692 ILE 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 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 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 56 ARG 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 103 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** B 143 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10773 Z= 0.204 Angle : 0.635 8.709 14545 Z= 0.320 Chirality : 0.044 0.156 1589 Planarity : 0.004 0.055 1859 Dihedral : 5.042 26.171 1402 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.30 % Allowed : 24.11 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1238 helix: -0.06 (0.38), residues: 215 sheet: -1.96 (0.41), residues: 141 loop : -1.23 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 412 HIS 0.010 0.001 HIS A 429 PHE 0.032 0.001 PHE A 258 TYR 0.028 0.001 TYR A 430 ARG 0.009 0.000 ARG E 50 *********************** 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 151 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 100 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.7239 (tpp) cc_final: 0.6806 (tpp) outliers start: 51 outliers final: 30 residues processed: 143 average time/residue: 0.2625 time to fit residues: 52.5718 Evaluate side-chains 120 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 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 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 109 LEU 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 364 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.0010 chunk 24 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10773 Z= 0.178 Angle : 0.627 10.692 14545 Z= 0.312 Chirality : 0.044 0.182 1589 Planarity : 0.004 0.054 1859 Dihedral : 4.894 27.010 1402 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.05 % Allowed : 24.45 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1238 helix: -0.06 (0.38), residues: 215 sheet: -1.83 (0.42), residues: 146 loop : -1.20 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 412 HIS 0.006 0.001 HIS A 429 PHE 0.029 0.001 PHE A 258 TYR 0.021 0.001 TYR A 430 ARG 0.009 0.000 ARG E 50 *********************** 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 142 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: B 294 MET cc_start: 0.7366 (tpp) cc_final: 0.6875 (tpp) outliers start: 48 outliers final: 30 residues processed: 132 average time/residue: 0.2782 time to fit residues: 50.6175 Evaluate side-chains 119 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 178 PHE 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 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 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 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 566 VAL 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 57 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10773 Z= 0.200 Angle : 0.642 10.659 14545 Z= 0.316 Chirality : 0.044 0.175 1589 Planarity : 0.004 0.053 1859 Dihedral : 4.851 25.515 1402 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.63 % Allowed : 25.04 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1238 helix: -0.19 (0.37), residues: 222 sheet: -1.67 (0.42), residues: 148 loop : -1.23 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 412 HIS 0.008 0.001 HIS A 429 PHE 0.023 0.001 PHE A 258 TYR 0.023 0.001 TYR A 430 ARG 0.013 0.001 ARG E 50 *********************** 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 138 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.7479 (tpp) cc_final: 0.7002 (tpp) REVERT: D 61 CYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7613 (t) REVERT: E 59 MET cc_start: 0.6306 (mpp) cc_final: 0.5943 (ptp) outliers start: 43 outliers final: 31 residues processed: 130 average time/residue: 0.2578 time to fit residues: 46.2954 Evaluate side-chains 122 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 90 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 104 LEU 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 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 315 LEU Chi-restraints excluded: chain A residue 417 HIS 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 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 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 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 548 HIS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 566 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 F residue 57 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.0020 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 691 GLN C 26 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10773 Z= 0.165 Angle : 0.641 11.095 14545 Z= 0.314 Chirality : 0.044 0.170 1589 Planarity : 0.004 0.056 1859 Dihedral : 4.695 24.736 1402 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.29 % Allowed : 25.89 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.24), residues: 1238 helix: -0.18 (0.37), residues: 223 sheet: -1.65 (0.44), residues: 136 loop : -1.21 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.005 0.000 HIS A 429 PHE 0.020 0.001 PHE A 258 TYR 0.022 0.001 TYR A 430 ARG 0.014 0.001 ARG E 50 *********************** 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 136 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 97 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 294 MET cc_start: 0.7511 (tpp) cc_final: 0.7034 (tpp) REVERT: B 552 LEU cc_start: 0.7966 (tt) cc_final: 0.7701 (tp) REVERT: D 61 CYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7401 (t) outliers start: 39 outliers final: 28 residues processed: 129 average time/residue: 0.2501 time to fit residues: 45.3765 Evaluate side-chains 120 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 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 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 566 VAL Chi-restraints excluded: chain B residue 21 HIS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 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 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 566 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 F residue 57 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.0570 chunk 76 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10773 Z= 0.167 Angle : 0.668 10.900 14545 Z= 0.325 Chirality : 0.044 0.173 1589 Planarity : 0.004 0.057 1859 Dihedral : 4.632 24.019 1402 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.87 % Allowed : 26.05 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1238 helix: -0.18 (0.37), residues: 223 sheet: -1.47 (0.44), residues: 143 loop : -1.22 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 412 HIS 0.033 0.001 HIS A 429 PHE 0.019 0.001 PHE C 16 TYR 0.054 0.001 TYR A 430 ARG 0.013 0.000 ARG E 50 *********************** 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 132 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.466 Fit side-chains revert: symmetry clash REVERT: A 430 TYR cc_start: 0.6803 (m-80) cc_final: 0.6538 (m-80) REVERT: B 294 MET cc_start: 0.7506 (tpp) cc_final: 0.7034 (tpp) REVERT: D 61 CYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7363 (t) outliers start: 34 outliers final: 27 residues processed: 124 average time/residue: 0.2658 time to fit residues: 45.7976 Evaluate side-chains 119 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 148 ASN Chi-restraints excluded: chain A residue 178 PHE 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 566 VAL Chi-restraints excluded: chain B residue 21 HIS 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 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 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 548 HIS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 566 VAL 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 F residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10773 Z= 0.229 Angle : 0.686 11.246 14545 Z= 0.339 Chirality : 0.045 0.174 1589 Planarity : 0.005 0.057 1859 Dihedral : 4.736 25.118 1402 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.61 % Allowed : 26.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.24), residues: 1238 helix: -0.16 (0.38), residues: 218 sheet: -1.55 (0.44), residues: 140 loop : -1.18 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 412 HIS 0.031 0.001 HIS A 429 PHE 0.016 0.001 PHE A 258 TYR 0.044 0.001 TYR A 430 ARG 0.014 0.001 ARG E 50 ********************** 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 126 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 TYR cc_start: 0.6912 (m-80) cc_final: 0.5554 (m-80) REVERT: B 294 MET cc_start: 0.7580 (tpp) cc_final: 0.7054 (tpp) REVERT: D 61 CYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7310 (t) outliers start: 31 outliers final: 28 residues processed: 121 average time/residue: 0.2680 time to fit residues: 45.0493 Evaluate side-chains 119 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 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 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 566 VAL Chi-restraints excluded: chain B residue 21 HIS 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 146 VAL Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 196 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 548 HIS Chi-restraints excluded: chain B residue 554 ARG Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain C residue 4 THR Chi-restraints excluded: chain D residue 24 TYR Chi-restraints excluded: chain D residue 61 CYS Chi-restraints excluded: chain F residue 57 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.0970 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.084777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.064968 restraints weight = 38437.591| |-----------------------------------------------------------------------------| 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: 0.8013 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10773 Z= 0.242 Angle : 0.688 11.330 14545 Z= 0.339 Chirality : 0.045 0.167 1589 Planarity : 0.004 0.054 1859 Dihedral : 4.824 25.515 1402 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.04 % Allowed : 26.48 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1238 helix: -0.11 (0.37), residues: 217 sheet: -1.61 (0.44), residues: 141 loop : -1.25 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 412 HIS 0.021 0.001 HIS A 429 PHE 0.019 0.001 PHE C 16 TYR 0.031 0.001 TYR A 430 ARG 0.013 0.001 ARG E 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2829.19 seconds wall clock time: 54 minutes 13.59 seconds (3253.59 seconds total)