Starting phenix.real_space_refine on Sun Jul 5 20:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nz0_48715/07_2026/9nz0_48715_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nz0_48715/07_2026/9nz0_48715.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/9nz0_48715/07_2026/9nz0_48715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nz0_48715/07_2026/9nz0_48715.map" model { file = "/net/cci-nas-00/data/ceres_data/9nz0_48715/07_2026/9nz0_48715_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nz0_48715/07_2026/9nz0_48715_neut_trim.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 9273 2.51 5 N 2442 2.21 5 O 2898 1.98 5 H 14565 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29253 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 6152 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 15, 'TRANS': 381} Chain breaks: 1 Chain: "D" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1803 Classifications: {'peptide': 119} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1768 Classifications: {'peptide': 114} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: B, C, F, I, G, H Time building chain proxies: 8.09, per 1000 atoms: 0.28 Number of scatterers: 29253 At special positions: 0 Unit cell: (149.6, 149.6, 176, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 2898 8.00 N 2442 7.00 C 9273 6.00 H 14565 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 387 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 350 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 387 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 387 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 412 " 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 65 " " NAG A 602 " - " ASN A 459 " " NAG B 601 " - " ASN B 65 " " NAG B 602 " - " ASN B 459 " " NAG C 601 " - " ASN C 65 " " NAG C 602 " - " ASN C 459 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 997.9 milliseconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3498 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 27.8% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 67 through 92 removed outlier: 3.637A pdb=" N PHE A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 149 through 186 removed outlier: 3.577A pdb=" N ASN A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Proline residue: A 180 - end of helix removed outlier: 3.583A pdb=" N GLN A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 215 Proline residue: A 211 - end of helix Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.618A pdb=" N LEU A 237 " --> pdb=" O ASN A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.337A pdb=" N ARG A 325 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 352 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 457 through 469 removed outlier: 4.106A pdb=" N THR A 461 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 67 through 92 removed outlier: 3.637A pdb=" N PHE B 71 " --> pdb=" O THR B 67 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 149 through 186 removed outlier: 3.576A pdb=" N ASN B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) Proline residue: B 180 - end of helix removed outlier: 3.583A pdb=" N GLN B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 215 Proline residue: B 211 - end of helix Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.617A pdb=" N LEU B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 Processing helix chain 'B' and resid 322 through 326 removed outlier: 4.336A pdb=" N ARG B 325 " --> pdb=" O ASP B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 352 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 457 through 469 removed outlier: 4.106A pdb=" N THR B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 67 through 92 removed outlier: 3.638A pdb=" N PHE C 71 " --> pdb=" O THR C 67 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 149 through 186 removed outlier: 3.576A pdb=" N ASN C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) Proline residue: C 180 - end of helix removed outlier: 3.582A pdb=" N GLN C 184 " --> pdb=" O PRO C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 215 Proline residue: C 211 - end of helix Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.618A pdb=" N LEU C 237 " --> pdb=" O ASN C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 255 Processing helix chain 'C' and resid 322 through 326 removed outlier: 4.336A pdb=" N ARG C 325 " --> pdb=" O ASP C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 352 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 457 through 469 removed outlier: 4.107A pdb=" N THR C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.762A pdb=" N GLY D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'D' and resid 83 through 87 removed outlier: 4.065A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.818A pdb=" N LEU E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.763A pdb=" N GLY F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 83 through 87 removed outlier: 4.065A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.818A pdb=" N LEU G 83 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.817A pdb=" N LEU H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.762A pdb=" N GLY I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 83 through 87 removed outlier: 4.066A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 removed outlier: 9.196A pdb=" N LYS A 42 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA A 286 " --> pdb=" O ASN A 40 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ASN A 40 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 288 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR A 38 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU A 290 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A 332 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 220 removed outlier: 3.800A pdb=" N GLY A 259 " --> pdb=" O THR A 219 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY A 259 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLU A 276 " --> pdb=" O GLY A 259 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 261 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 274 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP A 263 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 297 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 374 removed outlier: 4.590A pdb=" N VAL A 378 " --> pdb=" O LEU A 407 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 387 through 389 Processing sheet with id=AA6, first strand: chain 'A' and resid 431 through 433 removed outlier: 6.420A pdb=" N GLY A 431 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LYS B 55 " --> pdb=" O GLY A 431 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR A 433 " --> pdb=" O LYS B 55 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP B 263 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU B 274 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE B 261 " --> pdb=" O GLU B 274 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLU B 276 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY B 259 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY B 259 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 318 through 320 removed outlier: 9.195A pdb=" N LYS B 42 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA B 286 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN B 40 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 288 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR B 38 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU B 290 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 332 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 296 through 297 Processing sheet with id=AA9, first strand: chain 'B' and resid 371 through 374 removed outlier: 4.591A pdb=" N VAL B 378 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 387 through 389 Processing sheet with id=AB2, first strand: chain 'B' and resid 431 through 433 removed outlier: 6.435A pdb=" N GLY B 431 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LYS C 55 " --> pdb=" O GLY B 431 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B 433 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP C 263 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU C 274 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE C 261 " --> pdb=" O GLU C 274 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLU C 276 " --> pdb=" O GLY C 259 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY C 259 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY C 259 " --> pdb=" O THR C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 318 through 320 removed outlier: 9.196A pdb=" N LYS C 42 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA C 286 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN C 40 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL C 288 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR C 38 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N GLU C 290 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 332 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 296 through 297 Processing sheet with id=AB5, first strand: chain 'C' and resid 371 through 374 removed outlier: 4.591A pdb=" N VAL C 378 " --> pdb=" O LEU C 407 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 387 through 389 Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.500A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.568A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.625A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC6, first strand: chain 'F' and resid 18 through 23 Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.568A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.568A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.237A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.500A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 Processing sheet with id=AD6, first strand: chain 'I' and resid 18 through 23 647 hydrogen bonds defined for protein. 1713 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: 6.95 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14553 1.03 - 1.23: 18 1.23 - 1.42: 6144 1.42 - 1.62: 8685 1.62 - 1.81: 108 Bond restraints: 29508 Sorted by residual: bond pdb=" N SER A 22 " pdb=" CA SER A 22 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N SER C 22 " pdb=" CA SER C 22 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N SER B 22 " pdb=" CA SER B 22 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N SER A 22 " pdb=" H SER A 22 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" N SER B 22 " pdb=" H SER B 22 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 51859 1.26 - 2.51: 1325 2.51 - 3.77: 90 3.77 - 5.03: 6 5.03 - 6.29: 3 Bond angle restraints: 53283 Sorted by residual: angle pdb=" CA CYS A 187 " pdb=" CB CYS A 187 " pdb=" SG CYS A 187 " ideal model delta sigma weight residual 114.40 120.69 -6.29 2.30e+00 1.89e-01 7.47e+00 angle pdb=" CA CYS C 187 " pdb=" CB CYS C 187 " pdb=" SG CYS C 187 " ideal model delta sigma weight residual 114.40 120.67 -6.27 2.30e+00 1.89e-01 7.42e+00 angle pdb=" CA CYS B 187 " pdb=" CB CYS B 187 " pdb=" SG CYS B 187 " ideal model delta sigma weight residual 114.40 120.65 -6.25 2.30e+00 1.89e-01 7.39e+00 angle pdb=" CA VAL B 307 " pdb=" C VAL B 307 " pdb=" N PRO B 308 " ideal model delta sigma weight residual 116.57 119.21 -2.64 9.80e-01 1.04e+00 7.27e+00 angle pdb=" CA VAL A 307 " pdb=" C VAL A 307 " pdb=" N PRO A 308 " ideal model delta sigma weight residual 116.57 119.20 -2.63 9.80e-01 1.04e+00 7.20e+00 ... (remaining 53278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 12694 16.97 - 33.95: 974 33.95 - 50.92: 252 50.92 - 67.89: 81 67.89 - 84.86: 24 Dihedral angle restraints: 14025 sinusoidal: 7785 harmonic: 6240 Sorted by residual: dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual 93.00 177.86 -84.86 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS B 66 " pdb=" SG CYS B 66 " pdb=" SG CYS B 187 " pdb=" CB CYS B 187 " ideal model delta sinusoidal sigma weight residual 93.00 177.86 -84.86 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 187 " pdb=" CB CYS C 187 " ideal model delta sinusoidal sigma weight residual 93.00 177.85 -84.85 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 14022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1495 0.027 - 0.055: 566 0.055 - 0.082: 135 0.082 - 0.110: 107 0.110 - 0.137: 94 Chirality restraints: 2397 Sorted by residual: chirality pdb=" CA ILE A 451 " pdb=" N ILE A 451 " pdb=" C ILE A 451 " pdb=" CB ILE A 451 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA ILE C 451 " pdb=" N ILE C 451 " pdb=" C ILE C 451 " pdb=" CB ILE C 451 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE B 451 " pdb=" N ILE B 451 " pdb=" C ILE B 451 " pdb=" CB ILE B 451 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 2394 not shown) Planarity restraints: 4389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 100 " -0.010 2.00e-02 2.50e+03 6.77e-03 1.84e+00 pdb=" CG TRP I 100 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP I 100 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP I 100 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP I 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 100 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP I 100 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 100 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 100 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP I 100 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TRP I 100 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP I 100 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP I 100 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP I 100 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP I 100 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP I 100 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 100 " -0.010 2.00e-02 2.50e+03 6.69e-03 1.79e+00 pdb=" CG TRP F 100 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP F 100 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP F 100 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 100 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 100 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP F 100 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP F 100 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP F 100 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP F 100 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP F 100 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP F 100 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 292 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 293 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.018 5.00e-02 4.00e+02 ... (remaining 4386 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 14406 2.43 - 2.97: 65207 2.97 - 3.52: 69406 3.52 - 4.06: 95763 4.06 - 4.60: 140004 Nonbonded interactions: 384786 Sorted by model distance: nonbonded pdb="HE21 GLN G 6 " pdb=" H GLY G 101 " model vdw 1.889 2.100 nonbonded pdb="HE21 GLN H 6 " pdb=" H GLY H 101 " model vdw 1.889 2.100 nonbonded pdb="HE21 GLN E 6 " pdb=" H GLY E 101 " model vdw 1.889 2.100 nonbonded pdb="HH12 ARG A 171 " pdb="HD21 ASN A 175 " model vdw 1.891 2.100 nonbonded pdb="HH12 ARG B 171 " pdb="HD21 ASN B 175 " model vdw 1.892 2.100 ... (remaining 384781 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 3.340 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: 0.150 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 30.560 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 : 0.002 0.033 14964 Z= 0.093 Angle : 0.465 6.287 20361 Z= 0.265 Chirality : 0.042 0.137 2397 Planarity : 0.003 0.033 2574 Dihedral : 12.019 78.650 5544 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1866 helix: 2.81 (0.27), residues: 432 sheet: -0.10 (0.23), residues: 489 loop : -0.37 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 388 TYR 0.012 0.001 TYR E 49 PHE 0.005 0.000 PHE A 71 TRP 0.023 0.001 TRP I 100 HIS 0.001 0.000 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00177 / 0.09 (14943) covalent geometry : angle 0.45162 / 0.26 (20313) SS BOND : bond 0.00122 / 0.08 ( 15) SS BOND : angle 2.71594 / 1.22 ( 30) hydrogen bonds : bond 0.13653 / 8.91 ( 620) hydrogen bonds : angle 5.43798 / 4.01 ( 1713) link_NAG-ASN : bond 0.00289 / 0.17 ( 6) link_NAG-ASN : angle 1.49784 / 0.94 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 336 ASP cc_start: 0.8450 (m-30) cc_final: 0.8160 (t0) REVERT: F 13 LYS cc_start: 0.7085 (mttm) cc_final: 0.6827 (ttmt) REVERT: F 81 GLU cc_start: 0.8296 (tt0) cc_final: 0.7686 (tm-30) REVERT: F 100 TRP cc_start: 0.5905 (m-10) cc_final: 0.5406 (m-10) REVERT: G 29 ARG cc_start: 0.7199 (mpt180) cc_final: 0.6882 (mtp85) REVERT: G 87 TYR cc_start: 0.8130 (m-80) cc_final: 0.7925 (m-80) REVERT: H 29 ARG cc_start: 0.7325 (mpt180) cc_final: 0.6991 (mtp85) REVERT: I 13 LYS cc_start: 0.7321 (mttm) cc_final: 0.6974 (ttmt) outliers start: 0 outliers final: 0 residues processed: 278 average time/residue: 0.2639 time to fit residues: 108.1420 Evaluate side-chains 197 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 381 ASN B 384 ASN C 214 GLN G 6 GLN H 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.196948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163107 restraints weight = 53422.660| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.60 r_work: 0.3668 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14964 Z= 0.123 Angle : 0.497 8.319 20361 Z= 0.268 Chirality : 0.043 0.135 2397 Planarity : 0.004 0.033 2574 Dihedral : 4.036 19.486 2169 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.97 % Allowed : 3.81 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1866 helix: 2.61 (0.27), residues: 435 sheet: -0.18 (0.23), residues: 486 loop : -0.43 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.014 0.001 TYR H 49 PHE 0.008 0.001 PHE B 71 TRP 0.009 0.001 TRP F 100 HIS 0.002 0.001 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (14943) covalent geometry : angle 0.48266 / 0.26 (20313) SS BOND : bond 0.00419 / 0.27 ( 15) SS BOND : angle 3.04532 / 2.53 ( 30) hydrogen bonds : bond 0.03566 / 2.29 ( 620) hydrogen bonds : angle 4.64275 / 3.39 ( 1713) link_NAG-ASN : bond 0.00085 / 0.04 ( 6) link_NAG-ASN : angle 1.10978 / 0.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 30 ARG cc_start: 0.7586 (mtt180) cc_final: 0.7353 (mtt180) REVERT: E 103 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7995 (ttmm) REVERT: F 13 LYS cc_start: 0.7056 (mttm) cc_final: 0.6831 (ttmt) REVERT: F 57 ARG cc_start: 0.8335 (ptt-90) cc_final: 0.8081 (ptt90) REVERT: F 81 GLU cc_start: 0.8238 (tt0) cc_final: 0.7695 (tm-30) REVERT: G 29 ARG cc_start: 0.7260 (mpt180) cc_final: 0.6933 (mtp85) REVERT: H 29 ARG cc_start: 0.7310 (mpt180) cc_final: 0.7029 (mtp85) REVERT: I 13 LYS cc_start: 0.7312 (mttm) cc_final: 0.6963 (ttmt) REVERT: I 82 LEU cc_start: 0.8310 (mt) cc_final: 0.8071 (mm) outliers start: 16 outliers final: 14 residues processed: 212 average time/residue: 0.2682 time to fit residues: 82.5311 Evaluate side-chains 193 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain I residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 112 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 165 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.162194 restraints weight = 53346.657| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.57 r_work: 0.3573 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14964 Z= 0.106 Angle : 0.470 4.465 20361 Z= 0.254 Chirality : 0.043 0.136 2397 Planarity : 0.004 0.037 2574 Dihedral : 4.026 19.602 2169 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.03 % Allowed : 4.54 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.20), residues: 1866 helix: 2.55 (0.26), residues: 435 sheet: -0.25 (0.23), residues: 480 loop : -0.43 (0.20), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.013 0.001 TYR G 49 PHE 0.008 0.001 PHE A 71 TRP 0.007 0.001 TRP F 50 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (14943) covalent geometry : angle 0.46394 / 0.25 (20313) SS BOND : bond 0.00455 / 0.24 ( 15) SS BOND : angle 1.80876 / 1.44 ( 30) hydrogen bonds : bond 0.03148 / 2.03 ( 620) hydrogen bonds : angle 4.53563 / 3.30 ( 1713) link_NAG-ASN : bond 0.00103 / 0.05 ( 6) link_NAG-ASN : angle 1.07477 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 390 MET cc_start: 0.8024 (mmm) cc_final: 0.7788 (mmm) REVERT: E 103 LYS cc_start: 0.8394 (mtpp) cc_final: 0.7924 (ttmm) REVERT: F 13 LYS cc_start: 0.7084 (mttm) cc_final: 0.6853 (ttmt) REVERT: F 57 ARG cc_start: 0.8421 (ptt-90) cc_final: 0.8185 (ptt90) REVERT: F 81 GLU cc_start: 0.8284 (tt0) cc_final: 0.7520 (tm-30) REVERT: G 29 ARG cc_start: 0.7206 (mpt180) cc_final: 0.6676 (mtp85) REVERT: H 29 ARG cc_start: 0.7317 (mpt180) cc_final: 0.6905 (mtp85) REVERT: I 13 LYS cc_start: 0.7358 (mttm) cc_final: 0.7009 (ttmt) REVERT: I 79 TYR cc_start: 0.7457 (m-80) cc_final: 0.7202 (m-80) outliers start: 17 outliers final: 15 residues processed: 207 average time/residue: 0.2465 time to fit residues: 75.2244 Evaluate side-chains 195 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 384 ASN Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain I residue 70 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.193312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162884 restraints weight = 52803.091| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.53 r_work: 0.3530 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14964 Z= 0.121 Angle : 0.474 5.265 20361 Z= 0.258 Chirality : 0.043 0.138 2397 Planarity : 0.004 0.043 2574 Dihedral : 4.115 19.364 2169 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.39 % Allowed : 5.14 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.20), residues: 1866 helix: 2.46 (0.26), residues: 438 sheet: -0.39 (0.23), residues: 480 loop : -0.50 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 57 TYR 0.016 0.001 TYR E 49 PHE 0.008 0.001 PHE A 71 TRP 0.008 0.001 TRP F 50 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (14943) covalent geometry : angle 0.47122 / 0.26 (20313) SS BOND : bond 0.00343 / 0.20 ( 15) SS BOND : angle 1.24341 / 0.94 ( 30) hydrogen bonds : bond 0.03061 / 1.99 ( 620) hydrogen bonds : angle 4.50344 / 3.27 ( 1713) link_NAG-ASN : bond 0.00088 / 0.04 ( 6) link_NAG-ASN : angle 1.11901 / 0.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 LYS cc_start: 0.7125 (mttm) cc_final: 0.6903 (ttmt) REVERT: G 29 ARG cc_start: 0.7219 (mpt180) cc_final: 0.6778 (mtp85) REVERT: H 29 ARG cc_start: 0.7382 (mpt180) cc_final: 0.7011 (mtp85) REVERT: I 13 LYS cc_start: 0.7370 (mttm) cc_final: 0.7037 (ttmt) outliers start: 23 outliers final: 18 residues processed: 202 average time/residue: 0.2887 time to fit residues: 86.9173 Evaluate side-chains 198 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 70 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 156 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 GLN C 184 GLN D 35 HIS F 35 HIS I 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.185826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.156727 restraints weight = 53494.862| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.61 r_work: 0.3430 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 14964 Z= 0.278 Angle : 0.671 6.836 20361 Z= 0.374 Chirality : 0.048 0.186 2397 Planarity : 0.006 0.070 2574 Dihedral : 5.017 25.824 2169 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.03 % Allowed : 7.02 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 1866 helix: 1.68 (0.26), residues: 429 sheet: -0.72 (0.22), residues: 483 loop : -0.98 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 388 TYR 0.036 0.003 TYR H 49 PHE 0.010 0.002 PHE F 29 TRP 0.014 0.002 TRP B 303 HIS 0.006 0.002 HIS B 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00666 / 0.28 (14943) covalent geometry : angle 0.66382 / 0.37 (20313) SS BOND : bond 0.00677 / 0.44 ( 15) SS BOND : angle 2.47309 / 1.84 ( 30) hydrogen bonds : bond 0.04620 / 3.00 ( 620) hydrogen bonds : angle 5.23938 / 3.80 ( 1713) link_NAG-ASN : bond 0.00146 / 0.08 ( 6) link_NAG-ASN : angle 1.42473 / 0.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 LYS cc_start: 0.7282 (mttm) cc_final: 0.7020 (ttmt) REVERT: F 57 ARG cc_start: 0.8680 (ptt-90) cc_final: 0.8246 (ptt180) REVERT: G 29 ARG cc_start: 0.7461 (mpt180) cc_final: 0.6915 (mtp85) REVERT: H 29 ARG cc_start: 0.7629 (mpt180) cc_final: 0.7227 (mtp85) REVERT: I 13 LYS cc_start: 0.7431 (mttm) cc_final: 0.7090 (ttmt) outliers start: 17 outliers final: 17 residues processed: 211 average time/residue: 0.2993 time to fit residues: 93.9650 Evaluate side-chains 196 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 387 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 27 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 79 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 151 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 178 optimal weight: 4.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 297 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.188846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.164585 restraints weight = 53006.256| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.23 r_work: 0.3515 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14964 Z= 0.102 Angle : 0.485 5.802 20361 Z= 0.263 Chirality : 0.043 0.146 2397 Planarity : 0.004 0.053 2574 Dihedral : 4.498 22.470 2169 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.21 % Allowed : 7.68 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1866 helix: 2.16 (0.26), residues: 435 sheet: -0.63 (0.23), residues: 477 loop : -0.83 (0.20), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 57 TYR 0.016 0.001 TYR G 49 PHE 0.005 0.001 PHE B 71 TRP 0.009 0.001 TRP F 50 HIS 0.002 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 (14943) covalent geometry : angle 0.48065 / 0.26 (20313) SS BOND : bond 0.00428 / 0.25 ( 15) SS BOND : angle 1.51377 / 1.13 ( 30) hydrogen bonds : bond 0.03051 / 2.01 ( 620) hydrogen bonds : angle 4.70000 / 3.39 ( 1713) link_NAG-ASN : bond 0.00137 / 0.08 ( 6) link_NAG-ASN : angle 1.05759 / 0.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 LYS cc_start: 0.7231 (mttm) cc_final: 0.6992 (ttmt) REVERT: F 57 ARG cc_start: 0.8506 (ptt-90) cc_final: 0.8056 (ptt180) REVERT: G 29 ARG cc_start: 0.7227 (mpt180) cc_final: 0.6822 (mtp85) REVERT: H 29 ARG cc_start: 0.7358 (mpt180) cc_final: 0.7052 (mtp85) REVERT: H 105 GLU cc_start: 0.7282 (tm-30) cc_final: 0.6494 (tm-30) REVERT: I 13 LYS cc_start: 0.7335 (mttm) cc_final: 0.7021 (ttmt) outliers start: 20 outliers final: 20 residues processed: 197 average time/residue: 0.2985 time to fit residues: 86.3985 Evaluate side-chains 199 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 297 ASN Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 161 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.184687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153196 restraints weight = 53635.368| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.70 r_work: 0.3528 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14964 Z= 0.161 Angle : 0.521 4.811 20361 Z= 0.286 Chirality : 0.044 0.146 2397 Planarity : 0.004 0.055 2574 Dihedral : 4.549 24.186 2169 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.57 % Allowed : 7.74 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.19), residues: 1866 helix: 2.04 (0.26), residues: 435 sheet: -0.69 (0.23), residues: 477 loop : -0.91 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.022 0.002 TYR G 49 PHE 0.007 0.001 PHE B 71 TRP 0.010 0.001 TRP C 303 HIS 0.004 0.002 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (14943) covalent geometry : angle 0.51666 / 0.28 (20313) SS BOND : bond 0.00445 / 0.27 ( 15) SS BOND : angle 1.73061 / 1.25 ( 30) hydrogen bonds : bond 0.03487 / 2.28 ( 620) hydrogen bonds : angle 4.78821 / 3.46 ( 1713) link_NAG-ASN : bond 0.00089 / 0.04 ( 6) link_NAG-ASN : angle 1.11291 / 0.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7321 (tm-30) REVERT: F 13 LYS cc_start: 0.7277 (mttm) cc_final: 0.7031 (ttmt) REVERT: F 57 ARG cc_start: 0.8632 (ptt-90) cc_final: 0.8185 (ptt180) REVERT: G 29 ARG cc_start: 0.7418 (tpt170) cc_final: 0.6975 (mtp85) REVERT: H 29 ARG cc_start: 0.7520 (mpt180) cc_final: 0.7225 (mtp85) REVERT: H 105 GLU cc_start: 0.7375 (tm-30) cc_final: 0.6508 (tm-30) REVERT: I 13 LYS cc_start: 0.7387 (mttm) cc_final: 0.7059 (ttmt) outliers start: 26 outliers final: 22 residues processed: 203 average time/residue: 0.2883 time to fit residues: 87.5100 Evaluate side-chains 204 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 27 SER Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.0980 chunk 57 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 384 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.189179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159128 restraints weight = 53329.840| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.54 r_work: 0.3581 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14964 Z= 0.100 Angle : 0.474 4.726 20361 Z= 0.255 Chirality : 0.043 0.138 2397 Planarity : 0.004 0.049 2574 Dihedral : 4.359 22.380 2169 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.03 % Allowed : 8.53 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.20), residues: 1866 helix: 2.27 (0.26), residues: 438 sheet: -0.65 (0.23), residues: 474 loop : -0.80 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.014 0.001 TYR E 49 PHE 0.005 0.001 PHE B 71 TRP 0.009 0.001 TRP F 50 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (14943) covalent geometry : angle 0.46923 / 0.25 (20313) SS BOND : bond 0.00439 / 0.27 ( 15) SS BOND : angle 1.62603 / 1.31 ( 30) hydrogen bonds : bond 0.02869 / 1.89 ( 620) hydrogen bonds : angle 4.56860 / 3.30 ( 1713) link_NAG-ASN : bond 0.00126 / 0.07 ( 6) link_NAG-ASN : angle 0.99704 / 0.62 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 LYS cc_start: 0.7209 (mttm) cc_final: 0.6972 (ttmt) REVERT: F 57 ARG cc_start: 0.8534 (ptt-90) cc_final: 0.8064 (ptt180) REVERT: G 29 ARG cc_start: 0.7497 (tpt170) cc_final: 0.7067 (mtp85) REVERT: H 29 ARG cc_start: 0.7501 (tpt170) cc_final: 0.7300 (mtp85) REVERT: H 105 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6535 (tm-30) REVERT: I 13 LYS cc_start: 0.7325 (mttm) cc_final: 0.6998 (ttmt) outliers start: 17 outliers final: 16 residues processed: 197 average time/residue: 0.2910 time to fit residues: 85.7324 Evaluate side-chains 196 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 57 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.187622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.157600 restraints weight = 53084.814| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.64 r_work: 0.3433 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14964 Z= 0.167 Angle : 0.540 5.854 20361 Z= 0.295 Chirality : 0.044 0.148 2397 Planarity : 0.004 0.054 2574 Dihedral : 4.557 24.836 2169 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.21 % Allowed : 8.71 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.19), residues: 1866 helix: 2.17 (0.26), residues: 429 sheet: -0.80 (0.23), residues: 483 loop : -0.94 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.023 0.002 TYR E 49 PHE 0.008 0.001 PHE B 71 TRP 0.008 0.001 TRP B 303 HIS 0.004 0.002 HIS C 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (14943) covalent geometry : angle 0.53203 / 0.29 (20313) SS BOND : bond 0.00455 / 0.28 ( 15) SS BOND : angle 2.29143 / 1.77 ( 30) hydrogen bonds : bond 0.03524 / 2.31 ( 620) hydrogen bonds : angle 4.78628 / 3.46 ( 1713) link_NAG-ASN : bond 0.00098 / 0.05 ( 6) link_NAG-ASN : angle 1.08891 / 0.68 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 13 LYS cc_start: 0.7254 (mttm) cc_final: 0.6991 (ttmt) REVERT: F 57 ARG cc_start: 0.8611 (ptt-90) cc_final: 0.8171 (ptt180) REVERT: G 29 ARG cc_start: 0.7436 (tpt170) cc_final: 0.7003 (mtp85) REVERT: H 29 ARG cc_start: 0.7602 (tpt170) cc_final: 0.7306 (mtp85) REVERT: H 105 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6464 (tm-30) REVERT: I 13 LYS cc_start: 0.7410 (mttm) cc_final: 0.7084 (ttmt) outliers start: 20 outliers final: 20 residues processed: 202 average time/residue: 0.2678 time to fit residues: 79.4989 Evaluate side-chains 206 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 120 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 14 optimal weight: 0.0470 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.190467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.161530 restraints weight = 52805.278| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 1.38 r_work: 0.3497 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14964 Z= 0.096 Angle : 0.473 4.584 20361 Z= 0.256 Chirality : 0.043 0.140 2397 Planarity : 0.004 0.049 2574 Dihedral : 4.348 22.598 2169 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.09 % Allowed : 8.89 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1866 helix: 2.33 (0.26), residues: 438 sheet: -0.66 (0.23), residues: 474 loop : -0.84 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.013 0.001 TYR E 49 PHE 0.006 0.001 PHE B 71 TRP 0.010 0.001 TRP H 96 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14943) covalent geometry : angle 0.46833 / 0.25 (20313) SS BOND : bond 0.00386 / 0.23 ( 15) SS BOND : angle 1.72759 / 1.30 ( 30) hydrogen bonds : bond 0.02834 / 1.87 ( 620) hydrogen bonds : angle 4.56344 / 3.29 ( 1713) link_NAG-ASN : bond 0.00129 / 0.07 ( 6) link_NAG-ASN : angle 0.98393 / 0.61 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 GLN cc_start: 0.7802 (mp10) cc_final: 0.7474 (mp10) REVERT: F 13 LYS cc_start: 0.7239 (mttm) cc_final: 0.6985 (ttmt) REVERT: F 43 GLN cc_start: 0.7779 (mp10) cc_final: 0.7552 (mp10) REVERT: F 57 ARG cc_start: 0.8536 (ptt-90) cc_final: 0.8263 (ptt90) REVERT: G 29 ARG cc_start: 0.7268 (tpt170) cc_final: 0.6954 (mtp85) REVERT: H 29 ARG cc_start: 0.7425 (tpt170) cc_final: 0.7161 (mtp85) REVERT: I 13 LYS cc_start: 0.7372 (mttm) cc_final: 0.7044 (ttmt) REVERT: I 43 GLN cc_start: 0.7648 (mp10) cc_final: 0.7375 (mp10) outliers start: 18 outliers final: 18 residues processed: 201 average time/residue: 0.2694 time to fit residues: 80.4063 Evaluate side-chains 201 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 358 CYS Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 358 CYS Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain D residue 59 TYR Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain F residue 59 TYR Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 61 optimal weight: 0.7980 chunk 164 optimal weight: 0.0370 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.190137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159996 restraints weight = 53441.633| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.50 r_work: 0.3459 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14964 Z= 0.110 Angle : 0.487 5.894 20361 Z= 0.262 Chirality : 0.043 0.141 2397 Planarity : 0.004 0.049 2574 Dihedral : 4.311 22.901 2169 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.03 % Allowed : 9.38 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.20), residues: 1866 helix: 2.31 (0.26), residues: 438 sheet: -0.70 (0.23), residues: 474 loop : -0.84 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.016 0.001 TYR E 49 PHE 0.007 0.001 PHE B 71 TRP 0.009 0.001 TRP H 96 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (14943) covalent geometry : angle 0.48128 / 0.26 (20313) SS BOND : bond 0.00390 / 0.23 ( 15) SS BOND : angle 1.95130 / 1.43 ( 30) hydrogen bonds : bond 0.02928 / 1.93 ( 620) hydrogen bonds : angle 4.56198 / 3.29 ( 1713) link_NAG-ASN : bond 0.00108 / 0.05 ( 6) link_NAG-ASN : angle 0.95888 / 0.59 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7389.94 seconds wall clock time: 125 minutes 59.51 seconds (7559.51 seconds total)