Starting phenix.real_space_refine on Sat Nov 16 23:45:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kg5_37210/11_2024/8kg5_37210.cif" } resolution = 3.17 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= 0.001 sd= 0.020 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: 6 Type Number sf(0) Gaussians Br 6 7.06 5 S 77 5.16 5 Cl 3 4.86 5 C 7797 2.51 5 N 2020 2.21 5 O 2404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12307 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 12, 'TRANS': 436} Chain breaks: 1 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 950 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "E" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'336': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.92, per 1000 atoms: 0.64 Number of scatterers: 12307 At special positions: 0 Unit cell: (94.17, 100.01, 146.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 6 34.99 Cl 3 17.00 S 77 16.00 O 2404 8.00 N 2020 7.00 C 7797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.02 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.07 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.01 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.20 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.21 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.09 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.05 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.07 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.22 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.22 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.01 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.09 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.07 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.00 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.20 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.22 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.01 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: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 29 sheets defined 32.0% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.784A pdb=" N VAL A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.784A pdb=" N SER A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 4.118A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 282 Processing helix chain 'A' and resid 354 through 358 removed outlier: 3.654A pdb=" N CYS A 358 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 372 removed outlier: 3.580A pdb=" N ASN A 371 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 372' Processing helix chain 'A' and resid 376 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 492 through 512 removed outlier: 3.665A pdb=" N LEU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 95 Processing helix chain 'B' and resid 148 through 158 removed outlier: 3.799A pdb=" N VAL B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 172 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 208 through 213 removed outlier: 3.562A pdb=" N CYS B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 213' Processing helix chain 'B' and resid 216 through 227 removed outlier: 4.135A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.579A pdb=" N ASN B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 372 " --> pdb=" O THR B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 477 Processing helix chain 'B' and resid 492 through 512 removed outlier: 3.667A pdb=" N LEU B 512 " --> pdb=" O LYS B 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 95 Processing helix chain 'C' and resid 148 through 157 removed outlier: 3.661A pdb=" N VAL C 154 " --> pdb=" O SER C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 162 through 172 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.501A pdb=" N LYS C 209 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN C 210 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 227 removed outlier: 4.172A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 240 Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 282 Processing helix chain 'C' and resid 354 through 358 removed outlier: 3.654A pdb=" N CYS C 358 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 372 removed outlier: 3.579A pdb=" N ASN C 371 " --> pdb=" O ASP C 368 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 372 " --> pdb=" O THR C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.894A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 477 Processing helix chain 'C' and resid 492 through 512 removed outlier: 3.667A pdb=" N LEU C 512 " --> pdb=" O LYS C 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS A 359 " --> pdb=" O PHE A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER A 38 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU A 193 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 300 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N MET A 289 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLN A 302 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 287 " --> pdb=" O GLN A 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180 Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 406 removed outlier: 3.603A pdb=" N CYS A 416 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 359 " --> pdb=" O PHE B 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B 38 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU B 193 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB4, first strand: chain 'B' and resid 404 through 406 removed outlier: 4.075A pdb=" N CYS B 416 " --> pdb=" O GLY B 438 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS C 359 " --> pdb=" O PHE C 366 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 349 through 352 removed outlier: 7.025A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 38 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 193 through 194 removed outlier: 4.063A pdb=" N LEU C 193 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 64 through 66 removed outlier: 7.100A pdb=" N VAL D 100 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 180 Processing sheet with id=AC2, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AC3, first strand: chain 'C' and resid 404 through 406 removed outlier: 4.004A pdb=" N CYS C 416 " --> pdb=" O GLY C 438 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 438 " --> pdb=" O CYS C 416 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 431 through 434 removed outlier: 6.654A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.569A pdb=" N ALA D 93 " --> pdb=" O ASN D 35 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLY D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AC8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AD1, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.027A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.493A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.56 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 3446 1.33 - 1.49: 3406 1.49 - 1.64: 5546 1.64 - 1.79: 27 1.79 - 1.94: 84 Bond restraints: 12509 Sorted by residual: bond pdb=" C43 336 B 601 " pdb=" C49 336 B 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C43 336 A 601 " pdb=" C49 336 A 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.83e+01 bond pdb=" C43 336 C 601 " pdb=" C49 336 C 601 " ideal model delta sigma weight residual 1.532 1.367 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C49 336 B 601 " pdb=" C51 336 B 601 " ideal model delta sigma weight residual 1.531 1.375 0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C49 336 C 601 " pdb=" C51 336 C 601 " ideal model delta sigma weight residual 1.531 1.376 0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 12504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 16625 3.31 - 6.61: 297 6.61 - 9.92: 37 9.92 - 13.22: 3 13.22 - 16.53: 12 Bond angle restraints: 16974 Sorted by residual: angle pdb=" N ILE B 292 " pdb=" CA ILE B 292 " pdb=" C ILE B 292 " ideal model delta sigma weight residual 112.17 105.55 6.62 9.50e-01 1.11e+00 4.85e+01 angle pdb=" N CYS A 212 " pdb=" CA CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sigma weight residual 112.30 103.02 9.28 1.52e+00 4.33e-01 3.73e+01 angle pdb=" N ILE C 292 " pdb=" CA ILE C 292 " pdb=" C ILE C 292 " ideal model delta sigma weight residual 112.90 107.40 5.50 9.60e-01 1.09e+00 3.28e+01 angle pdb=" N VAL C 482 " pdb=" CA VAL C 482 " pdb=" C VAL C 482 " ideal model delta sigma weight residual 113.71 108.32 5.39 9.50e-01 1.11e+00 3.22e+01 angle pdb=" N VAL A 482 " pdb=" CA VAL A 482 " pdb=" C VAL A 482 " ideal model delta sigma weight residual 113.71 108.33 5.38 9.50e-01 1.11e+00 3.20e+01 ... (remaining 16969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.55: 7022 19.55 - 39.09: 534 39.09 - 58.64: 90 58.64 - 78.18: 32 78.18 - 97.73: 13 Dihedral angle restraints: 7691 sinusoidal: 3078 harmonic: 4613 Sorted by residual: dihedral pdb=" CB CYS A 416 " pdb=" SG CYS A 416 " pdb=" SG CYS A 422 " pdb=" CB CYS A 422 " ideal model delta sinusoidal sigma weight residual 93.00 -177.23 -89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 322 " pdb=" SG CYS B 322 " pdb=" SG CYS B 333 " pdb=" CB CYS B 333 " ideal model delta sinusoidal sigma weight residual 93.00 8.51 84.49 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS A 69 " pdb=" SG CYS A 69 " pdb=" SG CYS A 212 " pdb=" CB CYS A 212 " ideal model delta sinusoidal sigma weight residual -86.00 -163.19 77.19 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 7688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1818 0.097 - 0.193: 184 0.193 - 0.290: 16 0.290 - 0.387: 2 0.387 - 0.484: 3 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C49 336 C 601 " pdb=" C43 336 C 601 " pdb=" C51 336 C 601 " pdb=" C61 336 C 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C49 336 A 601 " pdb=" C43 336 A 601 " pdb=" C51 336 A 601 " pdb=" C61 336 A 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C49 336 B 601 " pdb=" C43 336 B 601 " pdb=" C51 336 B 601 " pdb=" C61 336 B 601 " both_signs ideal model delta sigma weight residual False -2.61 -2.13 -0.48 2.00e-01 2.50e+01 5.75e+00 ... (remaining 2020 not shown) Planarity restraints: 2129 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 91 " 0.080 2.00e-02 2.50e+03 5.57e-02 6.21e+01 pdb=" CG TYR E 91 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TYR E 91 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 91 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR E 91 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR E 91 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR E 91 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR E 91 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 35 " 0.083 2.00e-02 2.50e+03 4.97e-02 6.18e+01 pdb=" CG TRP E 35 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 35 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP E 35 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP E 35 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP E 35 " -0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP E 35 " -0.077 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 35 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 35 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 35 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 237 " -0.047 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE A 237 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 237 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 237 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE A 237 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 237 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 237 " -0.028 2.00e-02 2.50e+03 ... (remaining 2126 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1644 2.75 - 3.29: 12139 3.29 - 3.82: 19622 3.82 - 4.36: 24635 4.36 - 4.90: 42661 Nonbonded interactions: 100701 Sorted by model distance: nonbonded pdb=" O ILE E 2 " pdb=" OG1 THR E 97 " model vdw 2.212 3.040 nonbonded pdb=" OD2 ASP B 392 " pdb=" OG SER B 493 " model vdw 2.212 3.040 nonbonded pdb=" OG SER B 46 " pdb=" OG1 THR B 311 " model vdw 2.232 3.040 nonbonded pdb=" OG SER C 46 " pdb=" OG1 THR C 311 " model vdw 2.232 3.040 nonbonded pdb=" OG SER A 46 " pdb=" OG1 THR A 311 " model vdw 2.233 3.040 ... (remaining 100696 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' selection = chain 'B' selection = chain 'C' } 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.700 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 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 : 0.010 0.165 12509 Z= 0.634 Angle : 1.154 16.530 16974 Z= 0.664 Chirality : 0.061 0.484 2023 Planarity : 0.005 0.056 2129 Dihedral : 14.600 97.728 4639 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.49 % Allowed : 6.74 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.81 (0.18), residues: 1561 helix: -1.50 (0.22), residues: 438 sheet: -2.57 (0.21), residues: 435 loop : -3.12 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP E 35 HIS 0.016 0.003 HIS D 100G PHE 0.047 0.002 PHE A 237 TYR 0.105 0.003 TYR E 91 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 255 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.8045 (tp30) cc_final: 0.7468 (mm-30) REVERT: A 202 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7523 (tm-30) REVERT: B 80 LYS cc_start: 0.8436 (tttt) cc_final: 0.7518 (mmtt) REVERT: B 396 MET cc_start: 0.8311 (ptm) cc_final: 0.7862 (ttp) REVERT: C 427 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7984 (mtmm) REVERT: D 63 PHE cc_start: 0.8173 (m-80) cc_final: 0.7756 (m-80) outliers start: 7 outliers final: 2 residues processed: 259 average time/residue: 0.2660 time to fit residues: 97.1222 Evaluate side-chains 147 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain B residue 291 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 0.0020 chunk 89 optimal weight: 0.9980 chunk 139 optimal weight: 20.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 325 ASN A 361 GLN B 165 ASN B 361 GLN C 81 GLN C 210 GLN C 361 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN D 6 GLN D 35 ASN D 39 GLN D 100GHIS E 53 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12509 Z= 0.185 Angle : 0.673 10.278 16974 Z= 0.323 Chirality : 0.050 0.709 2023 Planarity : 0.004 0.042 2129 Dihedral : 10.030 105.919 1750 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.76 % Allowed : 10.67 % Favored : 87.57 % 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: -2.39 (0.20), residues: 1561 helix: 0.20 (0.25), residues: 441 sheet: -2.00 (0.22), residues: 429 loop : -2.48 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 159 PHE 0.020 0.001 PHE C 488 TYR 0.018 0.001 TYR A 417 ARG 0.005 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.598 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7966 (tp30) cc_final: 0.7640 (tp30) REVERT: A 171 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8289 (mp) REVERT: A 202 GLN cc_start: 0.7843 (tp-100) cc_final: 0.7524 (tm-30) REVERT: B 80 LYS cc_start: 0.8597 (tttt) cc_final: 0.7596 (mmtt) REVERT: B 97 MET cc_start: 0.4657 (mtm) cc_final: 0.4320 (mmm) REVERT: D 63 PHE cc_start: 0.8163 (m-80) cc_final: 0.7923 (m-80) REVERT: E 88 CYS cc_start: 0.7132 (p) cc_final: 0.6891 (p) outliers start: 25 outliers final: 15 residues processed: 194 average time/residue: 0.2442 time to fit residues: 69.5342 Evaluate side-chains 151 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 151 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN A 325 ASN B 81 GLN B 276 ASN C 325 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 12509 Z= 0.297 Angle : 0.703 10.630 16974 Z= 0.333 Chirality : 0.050 0.744 2023 Planarity : 0.004 0.041 2129 Dihedral : 9.980 108.470 1748 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.81 % Allowed : 12.85 % Favored : 84.34 % 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: -1.95 (0.20), residues: 1561 helix: 0.74 (0.26), residues: 435 sheet: -1.63 (0.20), residues: 509 loop : -2.42 (0.22), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.004 0.002 HIS A 317 PHE 0.012 0.001 PHE E 62 TYR 0.022 0.002 TYR A 417 ARG 0.005 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7973 (tp30) cc_final: 0.7699 (tp30) REVERT: A 88 ASN cc_start: 0.7653 (m-40) cc_final: 0.7413 (m-40) REVERT: B 97 MET cc_start: 0.4712 (mtm) cc_final: 0.4487 (mmm) REVERT: B 201 LYS cc_start: 0.7962 (mttt) cc_final: 0.7721 (mtmt) REVERT: B 251 MET cc_start: 0.8984 (mmp) cc_final: 0.8425 (mmp) REVERT: D 10 GLU cc_start: 0.6733 (tp30) cc_final: 0.6512 (tp30) REVERT: E 45 LYS cc_start: 0.7683 (tttt) cc_final: 0.7307 (tttm) REVERT: E 88 CYS cc_start: 0.7293 (p) cc_final: 0.6969 (p) outliers start: 40 outliers final: 27 residues processed: 168 average time/residue: 0.2599 time to fit residues: 65.3545 Evaluate side-chains 158 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 4.9990 chunk 105 optimal weight: 0.1980 chunk 72 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 140 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 chunk 73 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 94 GLN C 462 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12509 Z= 0.148 Angle : 0.615 11.191 16974 Z= 0.287 Chirality : 0.047 0.636 2023 Planarity : 0.003 0.039 2129 Dihedral : 9.772 104.405 1748 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.25 % Allowed : 14.26 % Favored : 83.50 % 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: -1.45 (0.21), residues: 1561 helix: 1.22 (0.27), residues: 438 sheet: -1.29 (0.21), residues: 512 loop : -2.27 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS D 100G PHE 0.012 0.001 PHE E 62 TYR 0.013 0.001 TYR B 299 ARG 0.004 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7854 (tp30) cc_final: 0.7574 (tp30) REVERT: A 202 GLN cc_start: 0.7878 (tp40) cc_final: 0.7060 (tm-30) REVERT: B 201 LYS cc_start: 0.7994 (mttt) cc_final: 0.7742 (mtmt) REVERT: E 45 LYS cc_start: 0.7696 (tttt) cc_final: 0.7358 (tttm) outliers start: 32 outliers final: 23 residues processed: 183 average time/residue: 0.2279 time to fit residues: 62.9273 Evaluate side-chains 157 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 325 ASN A 462 GLN B 325 ASN C 276 ASN C 462 GLN D 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 12509 Z= 0.450 Angle : 0.757 10.427 16974 Z= 0.358 Chirality : 0.053 0.801 2023 Planarity : 0.004 0.040 2129 Dihedral : 10.049 109.450 1748 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.02 % Allowed : 15.31 % Favored : 81.67 % 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: -1.70 (0.21), residues: 1561 helix: 0.77 (0.26), residues: 456 sheet: -1.44 (0.21), residues: 510 loop : -2.27 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 314 HIS 0.005 0.002 HIS A 317 PHE 0.014 0.002 PHE D 63 TYR 0.019 0.002 TYR C 441 ARG 0.005 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7971 (tp30) cc_final: 0.7733 (tp30) REVERT: B 202 GLN cc_start: 0.7904 (tp40) cc_final: 0.7289 (mp10) REVERT: B 251 MET cc_start: 0.8991 (mmp) cc_final: 0.8680 (mmp) REVERT: C 448 ASP cc_start: 0.7855 (m-30) cc_final: 0.7520 (m-30) REVERT: E 45 LYS cc_start: 0.7708 (tttt) cc_final: 0.7192 (tttm) outliers start: 43 outliers final: 30 residues processed: 159 average time/residue: 0.2411 time to fit residues: 59.5208 Evaluate side-chains 144 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 190 PHE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.9990 chunk 134 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12509 Z= 0.192 Angle : 0.636 11.127 16974 Z= 0.296 Chirality : 0.048 0.673 2023 Planarity : 0.003 0.040 2129 Dihedral : 9.860 106.727 1748 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.39 % Allowed : 16.57 % Favored : 81.04 % 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: -1.25 (0.21), residues: 1561 helix: 1.35 (0.27), residues: 438 sheet: -1.17 (0.21), residues: 512 loop : -2.11 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.009 0.001 PHE E 62 TYR 0.013 0.001 TYR B 299 ARG 0.005 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7863 (tp30) cc_final: 0.7556 (tp30) REVERT: B 202 GLN cc_start: 0.7923 (tp40) cc_final: 0.7285 (mp10) REVERT: E 45 LYS cc_start: 0.7715 (tttt) cc_final: 0.7187 (tttm) outliers start: 34 outliers final: 30 residues processed: 161 average time/residue: 0.2170 time to fit residues: 54.0652 Evaluate side-chains 151 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN A 462 GLN C 426 ASN C 462 GLN D 6 GLN D 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12509 Z= 0.200 Angle : 0.636 11.264 16974 Z= 0.295 Chirality : 0.048 0.662 2023 Planarity : 0.003 0.038 2129 Dihedral : 9.748 105.664 1748 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.74 % Allowed : 16.78 % Favored : 80.48 % 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: -1.05 (0.21), residues: 1561 helix: 1.55 (0.27), residues: 435 sheet: -1.03 (0.21), residues: 512 loop : -2.04 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.008 0.001 PHE E 62 TYR 0.014 0.001 TYR B 299 ARG 0.006 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7859 (tp30) cc_final: 0.7549 (tp30) REVERT: B 202 GLN cc_start: 0.7941 (tp40) cc_final: 0.7313 (mp10) REVERT: B 251 MET cc_start: 0.8971 (mmp) cc_final: 0.8651 (mmp) outliers start: 39 outliers final: 33 residues processed: 163 average time/residue: 0.2119 time to fit residues: 53.9872 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN D 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12509 Z= 0.194 Angle : 0.635 11.387 16974 Z= 0.294 Chirality : 0.047 0.643 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.727 105.570 1748 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.81 % Allowed : 17.06 % Favored : 80.13 % 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: -0.94 (0.21), residues: 1561 helix: 1.65 (0.27), residues: 435 sheet: -0.96 (0.22), residues: 512 loop : -1.98 (0.23), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.019 0.001 PHE B 505 TYR 0.019 0.001 TYR A 417 ARG 0.006 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 133 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7875 (tp30) cc_final: 0.7553 (tp30) REVERT: B 202 GLN cc_start: 0.7904 (tp40) cc_final: 0.7297 (mp10) REVERT: B 251 MET cc_start: 0.8967 (mmp) cc_final: 0.8617 (mmp) outliers start: 40 outliers final: 34 residues processed: 164 average time/residue: 0.2154 time to fit residues: 55.0906 Evaluate side-chains 159 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.0060 chunk 129 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 42 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12509 Z= 0.195 Angle : 0.634 11.462 16974 Z= 0.293 Chirality : 0.047 0.638 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.719 105.295 1748 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.06 % 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: -0.86 (0.22), residues: 1561 helix: 1.71 (0.27), residues: 435 sheet: -0.90 (0.22), residues: 512 loop : -1.93 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.010 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.007 0.000 ARG B 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7891 (tp30) cc_final: 0.7569 (tp30) REVERT: B 202 GLN cc_start: 0.7938 (tp40) cc_final: 0.7334 (mp10) outliers start: 36 outliers final: 34 residues processed: 160 average time/residue: 0.2137 time to fit residues: 52.5124 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 69 CYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 153 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12509 Z= 0.211 Angle : 0.646 11.487 16974 Z= 0.300 Chirality : 0.047 0.643 2023 Planarity : 0.003 0.036 2129 Dihedral : 9.737 105.551 1748 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.46 % Allowed : 17.70 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.82 (0.22), residues: 1561 helix: 1.74 (0.26), residues: 435 sheet: -0.89 (0.22), residues: 512 loop : -1.90 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 314 HIS 0.003 0.001 HIS A 317 PHE 0.021 0.001 PHE B 505 TYR 0.014 0.001 TYR B 299 ARG 0.007 0.000 ARG B 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3122 Ramachandran restraints generated. 1561 Oldfield, 0 Emsley, 1561 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 130 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7899 (tp30) cc_final: 0.7577 (tp30) REVERT: B 202 GLN cc_start: 0.7929 (tp40) cc_final: 0.7322 (mp10) outliers start: 35 outliers final: 33 residues processed: 158 average time/residue: 0.2043 time to fit residues: 50.7455 Evaluate side-chains 160 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 422 CYS Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 161 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 322 CYS Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 212 CYS Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 382 CYS Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 18 optimal weight: 0.0970 chunk 33 optimal weight: 0.0270 chunk 122 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN C 426 ASN C 462 GLN D 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.142102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105032 restraints weight = 14752.751| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.33 r_work: 0.3170 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12509 Z= 0.152 Angle : 0.618 11.708 16974 Z= 0.286 Chirality : 0.046 0.582 2023 Planarity : 0.003 0.037 2129 Dihedral : 9.730 104.360 1748 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.18 % Allowed : 18.05 % Favored : 79.78 % 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: -0.66 (0.22), residues: 1561 helix: 1.88 (0.27), residues: 435 sheet: -0.77 (0.22), residues: 512 loop : -1.83 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.002 0.001 HIS D 100G PHE 0.008 0.001 PHE D 63 TYR 0.014 0.001 TYR B 299 ARG 0.007 0.000 ARG B 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2833.00 seconds wall clock time: 52 minutes 51.41 seconds (3171.41 seconds total)