Starting phenix.real_space_refine on Thu Sep 26 22:25:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pls_13499/09_2024/7pls_13499.cif" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 9240 2.51 5 N 2332 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14224 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3529 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: C, B, D Time building chain proxies: 8.06, per 1000 atoms: 0.57 Number of scatterers: 14224 At special positions: 0 Unit cell: (159.714, 114.882, 59.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2612 8.00 N 2332 7.00 C 9240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.04 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 501 " - " ASN A 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.0 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 37.4% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 81 through 92 Processing helix chain 'A' and resid 97 through 105 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 199 through 205 Processing helix chain 'A' and resid 205 through 216 Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'B' and resid 35 through 40 Processing helix chain 'B' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 71 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 97 through 105 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 205 through 216 Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 236 through 247 Processing helix chain 'B' and resid 306 through 310 Processing helix chain 'B' and resid 312 through 326 Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 64 Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 81 through 92 Processing helix chain 'C' and resid 97 through 105 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 205 through 216 Processing helix chain 'C' and resid 231 through 236 Processing helix chain 'C' and resid 236 through 247 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 312 through 326 Processing helix chain 'C' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'D' and resid 35 through 40 Processing helix chain 'D' and resid 45 through 52 removed outlier: 4.311A pdb=" N ASP D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 Processing helix chain 'D' and resid 71 through 77 Processing helix chain 'D' and resid 81 through 92 Processing helix chain 'D' and resid 97 through 105 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 111 through 122 Processing helix chain 'D' and resid 158 through 170 removed outlier: 3.605A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 199 through 205 Processing helix chain 'D' and resid 205 through 216 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 236 through 247 Processing helix chain 'D' and resid 306 through 310 Processing helix chain 'D' and resid 312 through 326 Processing helix chain 'D' and resid 343 through 361 removed outlier: 3.712A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR A 174 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP A 223 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 176 " --> pdb=" O TRP A 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP A 225 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS A 178 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 127 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 129 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER A 179 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR A 131 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE A 53 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL A 128 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 55 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR A 130 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 57 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS A 132 " --> pdb=" O ILE A 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP A 370 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR A 383 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL A 372 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL A 381 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE A 455 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS A 415 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU A 457 " --> pdb=" O THR A 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR A 413 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY A 459 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 411 " --> pdb=" O GLY A 459 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR B 174 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP B 223 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU B 176 " --> pdb=" O TRP B 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP B 225 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS B 178 " --> pdb=" O ASP B 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL B 127 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 129 " --> pdb=" O TYR B 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER B 179 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR B 131 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE B 53 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL B 128 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 55 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR B 130 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE B 57 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS B 132 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP B 370 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR B 383 " --> pdb=" O TRP B 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL B 372 " --> pdb=" O VAL B 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL B 381 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE B 455 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS B 415 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU B 457 " --> pdb=" O THR B 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR B 413 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY B 459 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 411 " --> pdb=" O GLY B 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 402 through 405 Processing sheet with id=AA7, first strand: chain 'C' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR C 174 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP C 223 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU C 176 " --> pdb=" O TRP C 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP C 225 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS C 178 " --> pdb=" O ASP C 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 127 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR C 177 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 129 " --> pdb=" O TYR C 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER C 179 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR C 131 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE C 53 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL C 128 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 55 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR C 130 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE C 57 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS C 132 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP C 370 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR C 383 " --> pdb=" O TRP C 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL C 372 " --> pdb=" O VAL C 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL C 381 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE C 455 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS C 415 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU C 457 " --> pdb=" O THR C 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR C 413 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY C 459 " --> pdb=" O THR C 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR C 411 " --> pdb=" O GLY C 459 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 402 through 405 Processing sheet with id=AB1, first strand: chain 'D' and resid 255 through 256 removed outlier: 6.801A pdb=" N TYR D 174 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N TRP D 223 " --> pdb=" O TYR D 174 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU D 176 " --> pdb=" O TRP D 223 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ASP D 225 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS D 178 " --> pdb=" O ASP D 225 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL D 127 " --> pdb=" O GLY D 175 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR D 177 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 129 " --> pdb=" O TYR D 177 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N SER D 179 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N THR D 131 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N PHE D 53 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N VAL D 128 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL D 55 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N THR D 130 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE D 57 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N LYS D 132 " --> pdb=" O ILE D 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 368 through 374 removed outlier: 4.182A pdb=" N TRP D 370 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N TYR D 383 " --> pdb=" O TRP D 370 " (cutoff:3.500A) removed outlier: 9.205A pdb=" N VAL D 372 " --> pdb=" O VAL D 381 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N VAL D 381 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N ILE D 455 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 10.111A pdb=" N LYS D 415 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N LEU D 457 " --> pdb=" O THR D 413 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N THR D 413 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY D 459 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR D 411 " --> pdb=" O GLY D 459 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 402 through 405 488 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4104 1.34 - 1.46: 3588 1.46 - 1.58: 6972 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 14724 Sorted by residual: bond pdb=" N ILE D 317 " pdb=" CA ILE D 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE B 317 " pdb=" CA ILE B 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 317 " pdb=" CA ILE C 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE A 317 " pdb=" CA ILE A 317 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.67e+00 bond pdb=" N ILE C 316 " pdb=" CA ILE C 316 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.19e-02 7.06e+03 7.67e+00 ... (remaining 14719 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 19012 1.08 - 2.16: 804 2.16 - 3.24: 268 3.24 - 4.32: 40 4.32 - 5.40: 24 Bond angle restraints: 20148 Sorted by residual: angle pdb=" CA VAL B 321 " pdb=" C VAL B 321 " pdb=" O VAL B 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL A 321 " pdb=" C VAL A 321 " pdb=" O VAL A 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL C 321 " pdb=" C VAL C 321 " pdb=" O VAL C 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA VAL D 321 " pdb=" C VAL D 321 " pdb=" O VAL D 321 " ideal model delta sigma weight residual 121.17 118.11 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" O ILE D 317 " pdb=" C ILE D 317 " pdb=" N SER D 318 " ideal model delta sigma weight residual 121.87 124.66 -2.79 9.70e-01 1.06e+00 8.29e+00 ... (remaining 20143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 7369 17.16 - 34.32: 665 34.32 - 51.48: 261 51.48 - 68.64: 48 68.64 - 85.80: 28 Dihedral angle restraints: 8371 sinusoidal: 3375 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 274 " pdb=" CB CYS A 274 " ideal model delta sinusoidal sigma weight residual 93.00 58.32 34.68 1 1.00e+01 1.00e-02 1.71e+01 dihedral pdb=" CG ARG C 259 " pdb=" CD ARG C 259 " pdb=" NE ARG C 259 " pdb=" CZ ARG C 259 " ideal model delta sinusoidal sigma weight residual -180.00 -135.55 -44.45 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG D 259 " pdb=" CD ARG D 259 " pdb=" NE ARG D 259 " pdb=" CZ ARG D 259 " ideal model delta sinusoidal sigma weight residual 180.00 -135.55 -44.45 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 8368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1232 0.033 - 0.066: 492 0.066 - 0.099: 184 0.099 - 0.132: 100 0.132 - 0.165: 28 Chirality restraints: 2036 Sorted by residual: chirality pdb=" CA ILE B 316 " pdb=" N ILE B 316 " pdb=" C ILE B 316 " pdb=" CB ILE B 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA ILE C 316 " pdb=" N ILE C 316 " pdb=" C ILE C 316 " pdb=" CB ILE C 316 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2033 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG B 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG B 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG B 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG B 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " -0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG D 501 " 0.016 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " -0.045 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " 0.076 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 501 " 0.059 2.00e-02 2.50e+03 4.82e-02 2.91e+01 pdb=" C7 NAG A 501 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG A 501 " 0.045 2.00e-02 2.50e+03 pdb=" N2 NAG A 501 " -0.076 2.00e-02 2.50e+03 pdb=" O7 NAG A 501 " -0.012 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 97 2.61 - 3.18: 12070 3.18 - 3.76: 24016 3.76 - 4.33: 35850 4.33 - 4.90: 55912 Nonbonded interactions: 127945 Sorted by model distance: nonbonded pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " model vdw 2.039 3.760 nonbonded pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " model vdw 2.039 3.760 nonbonded pdb=" OE2 GLU B 362 " pdb=" OH TYR B 391 " model vdw 2.275 3.040 nonbonded pdb=" OE2 GLU C 362 " pdb=" OH TYR C 391 " model vdw 2.275 3.040 ... (remaining 127940 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.370 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:14.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14724 Z= 0.210 Angle : 0.578 5.397 20148 Z= 0.341 Chirality : 0.047 0.165 2036 Planarity : 0.005 0.048 2548 Dihedral : 16.349 85.803 5168 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.33 % Allowed : 12.00 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1716 helix: 0.95 (0.22), residues: 544 sheet: 0.21 (0.28), residues: 284 loop : -0.11 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 183 HIS 0.002 0.001 HIS C 134 PHE 0.012 0.001 PHE C 137 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG D 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.660 Fit side-chains REVERT: A 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: A 315 GLU cc_start: 0.7375 (tp30) cc_final: 0.7040 (tp30) REVERT: B 312 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: B 315 GLU cc_start: 0.7374 (tp30) cc_final: 0.7041 (tp30) REVERT: C 312 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: C 315 GLU cc_start: 0.7379 (tp30) cc_final: 0.7046 (tp30) REVERT: D 312 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6974 (mt-10) REVERT: D 315 GLU cc_start: 0.7373 (tp30) cc_final: 0.7038 (tp30) outliers start: 20 outliers final: 16 residues processed: 132 average time/residue: 1.1531 time to fit residues: 168.2923 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14724 Z= 0.327 Angle : 0.602 5.906 20148 Z= 0.317 Chirality : 0.049 0.147 2036 Planarity : 0.005 0.043 2548 Dihedral : 5.896 51.062 1976 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.67 % Allowed : 11.13 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1716 helix: 1.43 (0.23), residues: 524 sheet: -0.05 (0.29), residues: 292 loop : -0.35 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 243 HIS 0.003 0.001 HIS B 286 PHE 0.018 0.002 PHE D 137 TYR 0.014 0.002 TYR D 126 ARG 0.003 0.001 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.542 Fit side-chains REVERT: A 402 VAL cc_start: 0.7859 (t) cc_final: 0.7610 (t) REVERT: B 402 VAL cc_start: 0.7858 (t) cc_final: 0.7610 (t) REVERT: C 402 VAL cc_start: 0.7862 (t) cc_final: 0.7613 (t) REVERT: D 402 VAL cc_start: 0.7859 (t) cc_final: 0.7609 (t) outliers start: 25 outliers final: 8 residues processed: 136 average time/residue: 1.1920 time to fit residues: 179.8808 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 116 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14724 Z= 0.301 Angle : 0.598 6.122 20148 Z= 0.313 Chirality : 0.047 0.143 2036 Planarity : 0.005 0.046 2548 Dihedral : 4.671 20.567 1944 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.07 % Allowed : 11.93 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1716 helix: 1.45 (0.23), residues: 524 sheet: -0.33 (0.28), residues: 292 loop : -0.42 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 223 HIS 0.003 0.001 HIS A 156 PHE 0.017 0.002 PHE B 137 TYR 0.013 0.002 TYR B 126 ARG 0.003 0.000 ARG B 259 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 111 time to evaluate : 1.838 Fit side-chains REVERT: A 312 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: B 312 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: C 312 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: D 312 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7158 (mt-10) outliers start: 16 outliers final: 8 residues processed: 119 average time/residue: 1.3283 time to fit residues: 175.1146 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14724 Z= 0.200 Angle : 0.535 5.825 20148 Z= 0.278 Chirality : 0.045 0.140 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.343 17.181 1940 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.80 % Allowed : 12.27 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1716 helix: 1.58 (0.23), residues: 532 sheet: -0.36 (0.28), residues: 292 loop : -0.37 (0.22), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS D 156 PHE 0.011 0.002 PHE C 137 TYR 0.009 0.001 TYR A 126 ARG 0.001 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 1.672 Fit side-chains REVERT: A 312 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 312 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 312 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7140 (mt-10) REVERT: D 312 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7142 (mt-10) outliers start: 12 outliers final: 8 residues processed: 123 average time/residue: 1.3321 time to fit residues: 180.6386 Evaluate side-chains 123 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14724 Z= 0.242 Angle : 0.557 5.933 20148 Z= 0.291 Chirality : 0.046 0.142 2036 Planarity : 0.005 0.044 2548 Dihedral : 4.446 17.643 1940 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.27 % Allowed : 12.60 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1716 helix: 1.49 (0.23), residues: 532 sheet: -0.42 (0.28), residues: 292 loop : -0.40 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.002 0.001 HIS D 156 PHE 0.015 0.002 PHE D 137 TYR 0.012 0.001 TYR A 126 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 115 time to evaluate : 1.641 Fit side-chains REVERT: A 312 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: B 312 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7162 (mt-10) REVERT: C 312 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7159 (mt-10) REVERT: D 312 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7161 (mt-10) outliers start: 19 outliers final: 11 residues processed: 126 average time/residue: 1.2185 time to fit residues: 170.4387 Evaluate side-chains 130 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14724 Z= 0.194 Angle : 0.531 5.959 20148 Z= 0.275 Chirality : 0.044 0.138 2036 Planarity : 0.005 0.043 2548 Dihedral : 4.305 16.960 1940 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.20 % Allowed : 12.60 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.21), residues: 1716 helix: 1.52 (0.23), residues: 540 sheet: -0.39 (0.28), residues: 292 loop : -0.32 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 243 HIS 0.002 0.001 HIS A 267 PHE 0.012 0.002 PHE C 137 TYR 0.009 0.001 TYR A 126 ARG 0.002 0.000 ARG A 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.742 Fit side-chains REVERT: A 312 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7134 (mt-10) REVERT: B 312 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7135 (mt-10) REVERT: C 312 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: D 312 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7136 (mt-10) outliers start: 18 outliers final: 11 residues processed: 125 average time/residue: 1.2274 time to fit residues: 169.7590 Evaluate side-chains 134 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 312 GLU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 312 GLU Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14724 Z= 0.165 Angle : 0.509 5.604 20148 Z= 0.264 Chirality : 0.044 0.138 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.152 16.550 1940 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.80 % Allowed : 13.47 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1716 helix: 1.62 (0.23), residues: 540 sheet: -0.26 (0.28), residues: 288 loop : -0.28 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS B 156 PHE 0.010 0.001 PHE B 240 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 127 time to evaluate : 1.649 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 135 average time/residue: 1.2235 time to fit residues: 182.6270 Evaluate side-chains 126 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 114 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 81 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 144 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14724 Z= 0.155 Angle : 0.501 5.581 20148 Z= 0.259 Chirality : 0.043 0.139 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.071 16.206 1940 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.27 % Allowed : 13.00 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.21), residues: 1716 helix: 1.71 (0.23), residues: 540 sheet: -0.20 (0.29), residues: 288 loop : -0.24 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 243 HIS 0.002 0.001 HIS B 286 PHE 0.009 0.001 PHE C 96 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 118 time to evaluate : 1.564 Fit side-chains REVERT: A 400 ASN cc_start: 0.8494 (p0) cc_final: 0.8235 (p0) REVERT: B 400 ASN cc_start: 0.8496 (p0) cc_final: 0.8237 (p0) REVERT: C 400 ASN cc_start: 0.8504 (p0) cc_final: 0.8249 (p0) REVERT: D 400 ASN cc_start: 0.8497 (p0) cc_final: 0.8238 (p0) outliers start: 19 outliers final: 15 residues processed: 129 average time/residue: 1.3072 time to fit residues: 185.3413 Evaluate side-chains 130 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 ASN Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 171 ASN Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 171 ASN Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.1980 chunk 158 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14724 Z= 0.178 Angle : 0.518 5.635 20148 Z= 0.268 Chirality : 0.044 0.140 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.165 16.689 1940 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.00 % Allowed : 13.27 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1716 helix: 1.68 (0.23), residues: 540 sheet: -0.25 (0.28), residues: 288 loop : -0.24 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 243 HIS 0.002 0.001 HIS C 156 PHE 0.011 0.001 PHE B 240 TYR 0.009 0.001 TYR D 126 ARG 0.001 0.000 ARG D 259 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.732 Fit side-chains REVERT: A 400 ASN cc_start: 0.8472 (p0) cc_final: 0.8238 (p0) REVERT: B 400 ASN cc_start: 0.8474 (p0) cc_final: 0.8239 (p0) REVERT: C 400 ASN cc_start: 0.8492 (p0) cc_final: 0.8267 (p0) REVERT: D 400 ASN cc_start: 0.8475 (p0) cc_final: 0.8239 (p0) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 1.3522 time to fit residues: 187.1416 Evaluate side-chains 126 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 5.9990 chunk 77 optimal weight: 0.1980 chunk 113 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14724 Z= 0.398 Angle : 0.643 6.218 20148 Z= 0.339 Chirality : 0.050 0.146 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.740 18.932 1940 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.00 % Allowed : 13.27 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.20), residues: 1716 helix: 1.24 (0.23), residues: 548 sheet: -0.45 (0.28), residues: 292 loop : -0.40 (0.22), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 382 HIS 0.004 0.001 HIS B 156 PHE 0.025 0.003 PHE C 137 TYR 0.018 0.002 TYR B 126 ARG 0.003 0.001 ARG D 259 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.687 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 134 average time/residue: 1.2894 time to fit residues: 190.3003 Evaluate side-chains 126 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 266 CYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 266 CYS Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 266 CYS Chi-restraints excluded: chain D residue 429 THR Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.0570 chunk 119 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.086539 restraints weight = 14932.895| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.43 r_work: 0.2751 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14724 Z= 0.155 Angle : 0.520 9.810 20148 Z= 0.268 Chirality : 0.043 0.139 2036 Planarity : 0.005 0.042 2548 Dihedral : 4.230 16.221 1940 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.60 % Allowed : 13.40 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1716 helix: 1.62 (0.23), residues: 540 sheet: -0.30 (0.29), residues: 288 loop : -0.27 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 243 HIS 0.001 0.001 HIS C 111 PHE 0.010 0.001 PHE C 394 TYR 0.007 0.001 TYR D 126 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.62 seconds wall clock time: 72 minutes 15.24 seconds (4335.24 seconds total)