Starting phenix.real_space_refine on Tue Aug 6 04:11:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v62_42987/08_2024/8v62_42987.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 69 5.16 5 C 9585 2.51 5 N 2622 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15234 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 5 Chain: "B" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 5 Chain: "C" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 5 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "E" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "F" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "G" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "H" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "I" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 113} Time building chain proxies: 9.00, per 1000 atoms: 0.59 Number of scatterers: 15234 At special positions: 0 Unit cell: (135.36, 132.54, 127.84, 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 69 16.00 O 2958 8.00 N 2622 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.68 Conformation dependent library (CDL) restraints added in 2.7 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3648 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 39 sheets defined 29.1% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 215 removed outlier: 3.548A pdb=" N CYS A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 328 through 331 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 452 through 481 Processing helix chain 'B' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 137 Processing helix chain 'B' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP B 153 " --> pdb=" O GLU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 215 removed outlier: 3.547A pdb=" N CYS B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 238 through 243 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 328 through 331 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 452 through 481 Processing helix chain 'C' and resid 21 through 28 removed outlier: 3.538A pdb=" N GLN C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HIS C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 4.263A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 124 through 137 Processing helix chain 'C' and resid 137 through 154 removed outlier: 4.027A pdb=" N LYS C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.617A pdb=" N ILE C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.547A pdb=" N CYS C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 198 " --> pdb=" O ALA C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 235 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 452 through 481 Processing helix chain 'D' and resid 69 through 72 removed outlier: 3.718A pdb=" N LYS D 72 " --> pdb=" O ASP D 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 69 through 72' Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'E' and resid 69 through 72 removed outlier: 3.718A pdb=" N LYS E 72 " --> pdb=" O ASP E 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 69 through 72' Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'F' and resid 69 through 72 removed outlier: 3.717A pdb=" N LYS F 72 " --> pdb=" O ASP F 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 69 through 72' Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'G' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR G 99 " --> pdb=" O PRO G 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR H 99 " --> pdb=" O PRO H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 99 removed outlier: 3.901A pdb=" N THR I 99 " --> pdb=" O PRO I 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 158 through 160 removed outlier: 5.549A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ARG A 281 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL A 264 " --> pdb=" O ARG A 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE A 226 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 303 Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 160 removed outlier: 5.548A pdb=" N SER B 41 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 286 " --> pdb=" O SER B 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN B 43 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE B 226 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 158 through 160 Processing sheet with id=AB3, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AB4, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB5, first strand: chain 'B' and resid 301 through 303 Processing sheet with id=AB6, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB7, first strand: chain 'C' and resid 30 through 32 removed outlier: 4.577A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 158 through 160 removed outlier: 5.549A pdb=" N SER C 41 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N THR C 286 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASN C 43 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 268 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN C 279 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL C 266 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ARG C 281 " --> pdb=" O VAL C 264 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL C 264 " --> pdb=" O ARG C 281 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE C 226 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 158 through 160 Processing sheet with id=AC1, first strand: chain 'C' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AC3, first strand: chain 'C' and resid 392 through 394 Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER D 127 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 13 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA D 38 " --> pdb=" O ALA D 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET D 39 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG D 55 " --> pdb=" O MET D 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP D 41 " --> pdb=" O VAL D 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY D 11 " --> pdb=" O THR D 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER D 127 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL D 13 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.634A pdb=" N GLY E 11 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER E 127 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 38 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET E 39 " --> pdb=" O ARG E 55 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG E 55 " --> pdb=" O MET E 39 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP E 41 " --> pdb=" O VAL E 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 11 through 14 removed outlier: 6.634A pdb=" N GLY E 11 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N SER E 127 " --> pdb=" O GLY E 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL E 13 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AD2, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY F 11 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER F 127 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA F 38 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N MET F 39 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG F 55 " --> pdb=" O MET F 39 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TRP F 41 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.635A pdb=" N GLY F 11 " --> pdb=" O THR F 125 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N SER F 127 " --> pdb=" O GLY F 11 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL F 13 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 2 through 7 removed outlier: 3.534A pdb=" N THR G 77 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.169A pdb=" N GLY G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LYS G 37 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR G 57 " --> pdb=" O LYS G 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU G 39 " --> pdb=" O SER G 55 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER G 55 " --> pdb=" O LEU G 39 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TRP G 41 " --> pdb=" O VAL G 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 11 through 13 removed outlier: 6.169A pdb=" N GLY G 11 " --> pdb=" O THR G 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 2 through 7 removed outlier: 3.534A pdb=" N THR H 77 " --> pdb=" O ARG H 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N LYS H 37 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR H 57 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 39 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER H 55 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 2 through 7 removed outlier: 3.535A pdb=" N THR I 77 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N LYS I 37 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR I 57 " --> pdb=" O LYS I 37 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU I 39 " --> pdb=" O SER I 55 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N SER I 55 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 11 through 13 removed outlier: 6.168A pdb=" N GLY I 11 " --> pdb=" O THR I 125 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2061 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: 5.75 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5055 1.35 - 1.46: 3372 1.46 - 1.58: 6933 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 15450 Sorted by residual: bond pdb=" CB CYS A 195 " pdb=" SG CYS A 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.85e-01 bond pdb=" CB CYS C 195 " pdb=" SG CYS C 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.85e-01 bond pdb=" CB CYS B 195 " pdb=" SG CYS B 195 " ideal model delta sigma weight residual 1.808 1.785 0.023 3.30e-02 9.18e+02 4.84e-01 bond pdb=" CB VAL B 92 " pdb=" CG2 VAL B 92 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.45e-01 bond pdb=" CB VAL A 92 " pdb=" CG2 VAL A 92 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.20e-01 ... (remaining 15445 not shown) Histogram of bond angle deviations from ideal: 99.88 - 106.71: 315 106.71 - 113.54: 8665 113.54 - 120.37: 5328 120.37 - 127.20: 6507 127.20 - 134.03: 104 Bond angle restraints: 20919 Sorted by residual: angle pdb=" N SER A 174 " pdb=" CA SER A 174 " pdb=" C SER A 174 " ideal model delta sigma weight residual 111.02 114.60 -3.58 1.22e+00 6.72e-01 8.62e+00 angle pdb=" N SER C 174 " pdb=" CA SER C 174 " pdb=" C SER C 174 " ideal model delta sigma weight residual 111.02 114.58 -3.56 1.22e+00 6.72e-01 8.51e+00 angle pdb=" N SER B 174 " pdb=" CA SER B 174 " pdb=" C SER B 174 " ideal model delta sigma weight residual 111.02 114.53 -3.51 1.22e+00 6.72e-01 8.29e+00 angle pdb=" N VAL B 328 " pdb=" CA VAL B 328 " pdb=" CB VAL B 328 " ideal model delta sigma weight residual 111.82 105.51 6.31 2.75e+00 1.32e-01 5.26e+00 angle pdb=" N VAL C 328 " pdb=" CA VAL C 328 " pdb=" CB VAL C 328 " ideal model delta sigma weight residual 111.82 105.53 6.29 2.75e+00 1.32e-01 5.24e+00 ... (remaining 20914 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 8857 16.89 - 33.78: 448 33.78 - 50.66: 76 50.66 - 67.55: 12 67.55 - 84.44: 9 Dihedral angle restraints: 9402 sinusoidal: 3723 harmonic: 5679 Sorted by residual: dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 104 " pdb=" CB CYS G 104 " ideal model delta sinusoidal sigma weight residual 93.00 60.74 32.26 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 104 " pdb=" CB CYS I 104 " ideal model delta sinusoidal sigma weight residual 93.00 60.76 32.24 1 1.00e+01 1.00e-02 1.48e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 104 " pdb=" CB CYS H 104 " ideal model delta sinusoidal sigma weight residual 93.00 60.76 32.24 1 1.00e+01 1.00e-02 1.48e+01 ... (remaining 9399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1546 0.031 - 0.063: 547 0.063 - 0.094: 212 0.094 - 0.126: 140 0.126 - 0.157: 24 Chirality restraints: 2469 Sorted by residual: chirality pdb=" CA CYS C 195 " pdb=" N CYS C 195 " pdb=" C CYS C 195 " pdb=" CB CYS C 195 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA CYS A 195 " pdb=" N CYS A 195 " pdb=" C CYS A 195 " pdb=" CB CYS A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA CYS B 195 " pdb=" N CYS B 195 " pdb=" C CYS B 195 " pdb=" CB CYS B 195 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2466 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG I 43 " 0.163 9.50e-02 1.11e+02 7.38e-02 4.36e+00 pdb=" NE ARG I 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG I 43 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG I 43 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG I 43 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 43 " 0.162 9.50e-02 1.11e+02 7.32e-02 4.33e+00 pdb=" NE ARG G 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 43 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG G 43 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 43 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 43 " -0.162 9.50e-02 1.11e+02 7.33e-02 4.32e+00 pdb=" NE ARG H 43 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG H 43 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG H 43 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG H 43 " 0.000 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5293 2.87 - 3.38: 13766 3.38 - 3.89: 23956 3.89 - 4.39: 27080 4.39 - 4.90: 47428 Nonbonded interactions: 117523 Sorted by model distance: nonbonded pdb=" OD1 ASP A 204 " pdb=" NH2 ARG B 236 " model vdw 2.363 3.120 nonbonded pdb=" NE2 GLN B 403 " pdb=" O GLN B 407 " model vdw 2.367 3.120 nonbonded pdb=" NE2 GLN A 403 " pdb=" O GLN A 407 " model vdw 2.367 3.120 nonbonded pdb=" NE2 GLN C 403 " pdb=" O GLN C 407 " model vdw 2.368 3.120 nonbonded pdb=" OD1 ASP B 204 " pdb=" NH2 ARG C 236 " model vdw 2.372 3.120 ... (remaining 117518 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' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 2.020 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 43.560 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 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 0.027 15450 Z= 0.148 Angle : 0.561 6.308 20919 Z= 0.317 Chirality : 0.044 0.157 2469 Planarity : 0.007 0.074 2673 Dihedral : 10.429 84.440 5682 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.61 (0.19), residues: 1932 helix: 0.32 (0.23), residues: 441 sheet: 0.57 (0.21), residues: 594 loop : 0.53 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 118 HIS 0.001 0.000 HIS C 350 PHE 0.014 0.001 PHE A 346 TYR 0.020 0.004 TYR B 338 ARG 0.018 0.003 ARG G 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 477 time to evaluate : 1.852 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: A 36 LYS cc_start: 0.8360 (mttt) cc_final: 0.7951 (mttt) REVERT: A 49 LEU cc_start: 0.8748 (tp) cc_final: 0.8518 (tt) REVERT: A 57 ILE cc_start: 0.8670 (mm) cc_final: 0.8273 (mm) REVERT: A 65 ASP cc_start: 0.7940 (p0) cc_final: 0.7732 (p0) REVERT: A 69 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8596 (ttmm) REVERT: A 70 GLN cc_start: 0.8498 (tp40) cc_final: 0.8196 (tp-100) REVERT: A 73 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7817 (ttm110) REVERT: A 74 LEU cc_start: 0.8668 (tp) cc_final: 0.8229 (tp) REVERT: A 139 GLN cc_start: 0.7704 (tp40) cc_final: 0.7390 (tp-100) REVERT: A 175 VAL cc_start: 0.8395 (m) cc_final: 0.7999 (t) REVERT: A 182 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 193 GLU cc_start: 0.8459 (pm20) cc_final: 0.8192 (pm20) REVERT: A 205 GLN cc_start: 0.8069 (mt0) cc_final: 0.7796 (mt0) REVERT: A 207 TYR cc_start: 0.8533 (t80) cc_final: 0.8176 (t80) REVERT: A 212 ASN cc_start: 0.8082 (t0) cc_final: 0.7869 (t0) REVERT: A 229 GLN cc_start: 0.8155 (tp40) cc_final: 0.7841 (tp40) REVERT: A 263 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7964 (mtpt) REVERT: A 270 ASP cc_start: 0.7785 (t0) cc_final: 0.7484 (t0) REVERT: A 294 TYR cc_start: 0.8197 (m-80) cc_final: 0.7971 (m-80) REVERT: A 333 GLU cc_start: 0.7810 (tt0) cc_final: 0.7412 (tt0) REVERT: A 432 GLU cc_start: 0.7454 (mp0) cc_final: 0.7075 (mp0) REVERT: B 36 LYS cc_start: 0.8337 (mttt) cc_final: 0.8135 (mttt) REVERT: B 70 GLN cc_start: 0.8595 (tp40) cc_final: 0.8227 (tp40) REVERT: B 73 ARG cc_start: 0.8250 (ttm110) cc_final: 0.8003 (ttm110) REVERT: B 74 LEU cc_start: 0.8671 (tp) cc_final: 0.8406 (tp) REVERT: B 90 LYS cc_start: 0.7416 (mmtt) cc_final: 0.7148 (mmtt) REVERT: B 139 GLN cc_start: 0.7748 (tp40) cc_final: 0.7510 (tp40) REVERT: B 151 ILE cc_start: 0.8469 (mt) cc_final: 0.8242 (tp) REVERT: B 158 VAL cc_start: 0.8657 (t) cc_final: 0.8272 (p) REVERT: B 175 VAL cc_start: 0.8304 (m) cc_final: 0.8017 (t) REVERT: B 212 ASN cc_start: 0.8066 (t0) cc_final: 0.7417 (t0) REVERT: B 214 PHE cc_start: 0.8303 (m-80) cc_final: 0.7997 (m-80) REVERT: B 238 ASN cc_start: 0.7680 (m-40) cc_final: 0.7449 (m-40) REVERT: B 256 LEU cc_start: 0.7921 (mm) cc_final: 0.7641 (mm) REVERT: B 263 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7783 (mtpt) REVERT: B 281 ARG cc_start: 0.8113 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: B 332 ILE cc_start: 0.8427 (mm) cc_final: 0.8226 (mt) REVERT: B 375 ARG cc_start: 0.8483 (mtt90) cc_final: 0.8268 (mtt90) REVERT: B 431 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7550 (mmtt) REVERT: B 432 GLU cc_start: 0.7207 (mp0) cc_final: 0.6613 (mp0) REVERT: B 464 LYS cc_start: 0.8345 (mtpp) cc_final: 0.8026 (mtpp) REVERT: B 468 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 469 GLU cc_start: 0.8244 (tt0) cc_final: 0.7941 (tt0) REVERT: B 471 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7424 (ttmm) REVERT: C 36 LYS cc_start: 0.8386 (mttt) cc_final: 0.8142 (mttt) REVERT: C 38 MET cc_start: 0.8401 (ttp) cc_final: 0.8090 (ttp) REVERT: C 69 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8560 (ttmm) REVERT: C 73 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7841 (ttm110) REVERT: C 83 TYR cc_start: 0.8287 (t80) cc_final: 0.8016 (t80) REVERT: C 89 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7001 (pt0) REVERT: C 177 ASP cc_start: 0.8273 (t70) cc_final: 0.8073 (t0) REVERT: C 212 ASN cc_start: 0.8194 (t0) cc_final: 0.7711 (t0) REVERT: C 262 ILE cc_start: 0.8156 (mt) cc_final: 0.7916 (mm) REVERT: C 275 SER cc_start: 0.8646 (t) cc_final: 0.8416 (p) REVERT: C 297 ASP cc_start: 0.7745 (m-30) cc_final: 0.7494 (m-30) REVERT: C 307 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7491 (mt-10) REVERT: C 314 SER cc_start: 0.8516 (m) cc_final: 0.8291 (p) REVERT: C 375 ARG cc_start: 0.8426 (mtt90) cc_final: 0.7987 (mtt90) REVERT: C 464 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7973 (mttm) REVERT: E 64 THR cc_start: 0.8707 (m) cc_final: 0.8292 (p) REVERT: H 28 SER cc_start: 0.8513 (m) cc_final: 0.8229 (p) REVERT: I 28 SER cc_start: 0.8546 (m) cc_final: 0.8178 (p) outliers start: 0 outliers final: 0 residues processed: 477 average time/residue: 0.2930 time to fit residues: 197.5418 Evaluate side-chains 431 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 0.0060 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.0770 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 27 HIS A 89 GLN A 305 ASN A 380 ASN A 446 ASN A 479 GLN B 19 GLN B 89 GLN B 127 GLN B 159 GLN B 305 ASN B 380 ASN B 479 GLN C 19 GLN C 89 GLN C 127 GLN C 238 ASN C 305 ASN C 380 ASN C 479 GLN D 116 ASN E 116 ASN F 116 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15450 Z= 0.199 Angle : 0.536 6.192 20919 Z= 0.290 Chirality : 0.044 0.150 2469 Planarity : 0.004 0.035 2673 Dihedral : 4.770 83.588 2136 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.19 % Allowed : 7.68 % Favored : 90.13 % 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: 1.01 (0.19), residues: 1932 helix: 1.24 (0.25), residues: 450 sheet: 0.58 (0.22), residues: 585 loop : 0.62 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 118 HIS 0.003 0.001 HIS B 206 PHE 0.011 0.001 PHE A 346 TYR 0.018 0.002 TYR B 207 ARG 0.004 0.000 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 431 time to evaluate : 1.751 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: A 45 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 49 LEU cc_start: 0.8687 (tp) cc_final: 0.8448 (tt) REVERT: A 57 ILE cc_start: 0.8680 (mm) cc_final: 0.8335 (mm) REVERT: A 66 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7294 (tm-30) REVERT: A 70 GLN cc_start: 0.8532 (tp40) cc_final: 0.7918 (tp40) REVERT: A 73 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7708 (ttm110) REVERT: A 182 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7646 (mt-10) REVERT: A 190 LEU cc_start: 0.8791 (mt) cc_final: 0.8528 (mp) REVERT: A 205 GLN cc_start: 0.8056 (mt0) cc_final: 0.7817 (mt0) REVERT: A 229 GLN cc_start: 0.8127 (tp40) cc_final: 0.7681 (tp-100) REVERT: A 263 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7969 (mtpt) REVERT: A 265 ARG cc_start: 0.7695 (ptm160) cc_final: 0.7459 (ptm160) REVERT: A 270 ASP cc_start: 0.7702 (t0) cc_final: 0.7380 (t0) REVERT: A 331 CYS cc_start: 0.7492 (m) cc_final: 0.7287 (m) REVERT: A 432 GLU cc_start: 0.7484 (mp0) cc_final: 0.7119 (mp0) REVERT: B 63 CYS cc_start: 0.7413 (t) cc_final: 0.7178 (t) REVERT: B 65 ASP cc_start: 0.7772 (p0) cc_final: 0.7473 (p0) REVERT: B 73 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7624 (ttm110) REVERT: B 212 ASN cc_start: 0.8026 (t0) cc_final: 0.7483 (t0) REVERT: B 214 PHE cc_start: 0.8197 (m-80) cc_final: 0.7917 (m-80) REVERT: B 263 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7776 (mtpt) REVERT: B 272 ASN cc_start: 0.7942 (m-40) cc_final: 0.7666 (m-40) REVERT: B 281 ARG cc_start: 0.8039 (mtm-85) cc_final: 0.7641 (mtm-85) REVERT: B 296 VAL cc_start: 0.8209 (t) cc_final: 0.7955 (m) REVERT: B 331 CYS cc_start: 0.7400 (m) cc_final: 0.7199 (m) REVERT: B 375 ARG cc_start: 0.8454 (mtt90) cc_final: 0.8230 (mtt90) REVERT: B 432 GLU cc_start: 0.7224 (mp0) cc_final: 0.6645 (mp0) REVERT: B 469 GLU cc_start: 0.8204 (tt0) cc_final: 0.7907 (tt0) REVERT: B 471 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7436 (ttmm) REVERT: C 38 MET cc_start: 0.8372 (ttp) cc_final: 0.8159 (ttp) REVERT: C 65 ASP cc_start: 0.7711 (p0) cc_final: 0.7489 (p0) REVERT: C 69 LYS cc_start: 0.8790 (ttmm) cc_final: 0.8498 (ttmm) REVERT: C 76 ASP cc_start: 0.7902 (m-30) cc_final: 0.7504 (m-30) REVERT: C 83 TYR cc_start: 0.8215 (t80) cc_final: 0.7943 (t80) REVERT: C 177 ASP cc_start: 0.8243 (t70) cc_final: 0.8035 (t0) REVERT: C 212 ASN cc_start: 0.8164 (t0) cc_final: 0.7793 (t0) REVERT: C 260 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7576 (mm-30) REVERT: C 262 ILE cc_start: 0.8184 (mt) cc_final: 0.7908 (mm) REVERT: C 270 ASP cc_start: 0.7846 (t0) cc_final: 0.7614 (t0) REVERT: C 274 TYR cc_start: 0.8637 (m-80) cc_final: 0.7951 (m-80) REVERT: C 297 ASP cc_start: 0.7792 (m-30) cc_final: 0.7495 (m-30) REVERT: C 314 SER cc_start: 0.8476 (m) cc_final: 0.8244 (p) REVERT: C 353 GLU cc_start: 0.7189 (tt0) cc_final: 0.6821 (tt0) REVERT: C 464 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7962 (mttm) REVERT: C 469 GLU cc_start: 0.8203 (tt0) cc_final: 0.7956 (tp30) REVERT: G 118 TRP cc_start: 0.8491 (m100) cc_final: 0.7960 (m100) REVERT: H 28 SER cc_start: 0.8596 (m) cc_final: 0.8239 (p) outliers start: 37 outliers final: 22 residues processed: 446 average time/residue: 0.3077 time to fit residues: 191.9697 Evaluate side-chains 432 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 410 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 188 optimal weight: 0.0970 chunk 155 optimal weight: 0.7980 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN A 399 ASN A 403 GLN B 205 GLN B 380 ASN C 305 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15450 Z= 0.247 Angle : 0.536 6.757 20919 Z= 0.283 Chirality : 0.044 0.149 2469 Planarity : 0.004 0.034 2673 Dihedral : 4.888 82.935 2136 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.30 % Allowed : 10.17 % Favored : 87.53 % 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: 0.99 (0.19), residues: 1932 helix: 1.46 (0.25), residues: 450 sheet: 0.50 (0.21), residues: 576 loop : 0.52 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 118 HIS 0.001 0.000 HIS C 315 PHE 0.013 0.002 PHE B 427 TYR 0.016 0.002 TYR B 294 ARG 0.006 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 418 time to evaluate : 1.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7703 (mm-30) REVERT: A 57 ILE cc_start: 0.8721 (mm) cc_final: 0.8356 (mm) REVERT: A 66 GLN cc_start: 0.7711 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 70 GLN cc_start: 0.8580 (tp40) cc_final: 0.7977 (tp40) REVERT: A 73 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7715 (ttm110) REVERT: A 182 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 190 LEU cc_start: 0.8897 (mt) cc_final: 0.8646 (mp) REVERT: A 205 GLN cc_start: 0.8063 (mt0) cc_final: 0.7833 (mt0) REVERT: A 263 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7975 (mtpt) REVERT: A 270 ASP cc_start: 0.7635 (t0) cc_final: 0.7313 (t0) REVERT: A 294 TYR cc_start: 0.8622 (m-80) cc_final: 0.8233 (m-80) REVERT: A 331 CYS cc_start: 0.7467 (m) cc_final: 0.7231 (m) REVERT: A 432 GLU cc_start: 0.7498 (mp0) cc_final: 0.7149 (mp0) REVERT: A 462 LYS cc_start: 0.7962 (tptt) cc_final: 0.7745 (tptt) REVERT: B 63 CYS cc_start: 0.7533 (t) cc_final: 0.7280 (t) REVERT: B 70 GLN cc_start: 0.8601 (tp40) cc_final: 0.8355 (tp-100) REVERT: B 73 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7747 (ttm110) REVERT: B 212 ASN cc_start: 0.8101 (t0) cc_final: 0.7550 (t0) REVERT: B 214 PHE cc_start: 0.8262 (m-80) cc_final: 0.7959 (m-80) REVERT: B 238 ASN cc_start: 0.7653 (m-40) cc_final: 0.7377 (m-40) REVERT: B 263 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7768 (mtpt) REVERT: B 281 ARG cc_start: 0.8044 (mtm-85) cc_final: 0.7666 (mtm-85) REVERT: B 296 VAL cc_start: 0.8237 (t) cc_final: 0.7979 (m) REVERT: B 365 ARG cc_start: 0.8378 (ptt90) cc_final: 0.8169 (ptt-90) REVERT: B 432 GLU cc_start: 0.7267 (mp0) cc_final: 0.6683 (mp0) REVERT: B 469 GLU cc_start: 0.8200 (tt0) cc_final: 0.7944 (tt0) REVERT: B 471 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7432 (ttmm) REVERT: C 21 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: C 38 MET cc_start: 0.8402 (ttp) cc_final: 0.8201 (ttp) REVERT: C 69 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8524 (ttmm) REVERT: C 73 ARG cc_start: 0.8098 (ttm110) cc_final: 0.7812 (ttm110) REVERT: C 83 TYR cc_start: 0.8205 (t80) cc_final: 0.7957 (t80) REVERT: C 89 GLN cc_start: 0.7607 (tp40) cc_final: 0.7016 (pt0) REVERT: C 92 VAL cc_start: 0.7321 (m) cc_final: 0.6967 (p) REVERT: C 177 ASP cc_start: 0.8254 (t70) cc_final: 0.8032 (t0) REVERT: C 212 ASN cc_start: 0.8142 (t0) cc_final: 0.7811 (t0) REVERT: C 262 ILE cc_start: 0.8139 (mt) cc_final: 0.7853 (mm) REVERT: C 297 ASP cc_start: 0.7789 (m-30) cc_final: 0.7498 (m-30) REVERT: C 314 SER cc_start: 0.8442 (m) cc_final: 0.8201 (p) REVERT: C 469 GLU cc_start: 0.8196 (tt0) cc_final: 0.7945 (tp30) REVERT: H 28 SER cc_start: 0.8616 (m) cc_final: 0.8277 (p) outliers start: 39 outliers final: 26 residues processed: 433 average time/residue: 0.2994 time to fit residues: 181.8092 Evaluate side-chains 421 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 394 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 7.9990 chunk 131 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 305 ASN A 380 ASN A 403 GLN B 305 ASN B 380 ASN C 279 GLN C 305 ASN C 446 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 15450 Z= 0.297 Angle : 0.548 7.854 20919 Z= 0.289 Chirality : 0.045 0.159 2469 Planarity : 0.004 0.041 2673 Dihedral : 5.025 81.989 2136 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.96 % Allowed : 11.23 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.19), residues: 1932 helix: 1.38 (0.25), residues: 450 sheet: 0.34 (0.21), residues: 585 loop : 0.41 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 118 HIS 0.001 0.000 HIS B 206 PHE 0.017 0.002 PHE B 427 TYR 0.018 0.002 TYR B 294 ARG 0.005 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 410 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 57 ILE cc_start: 0.8715 (mm) cc_final: 0.8394 (mm) REVERT: A 66 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 70 GLN cc_start: 0.8593 (tp40) cc_final: 0.8071 (tp-100) REVERT: A 73 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7736 (ttm110) REVERT: A 182 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 190 LEU cc_start: 0.8997 (mt) cc_final: 0.8741 (mp) REVERT: A 205 GLN cc_start: 0.8102 (mt0) cc_final: 0.7870 (mt0) REVERT: A 263 LYS cc_start: 0.8185 (mtpt) cc_final: 0.7969 (mtpt) REVERT: A 270 ASP cc_start: 0.7610 (t0) cc_final: 0.7272 (t0) REVERT: A 331 CYS cc_start: 0.7474 (m) cc_final: 0.7230 (m) REVERT: A 432 GLU cc_start: 0.7505 (mp0) cc_final: 0.7157 (mp0) REVERT: A 459 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 70 GLN cc_start: 0.8576 (tp40) cc_final: 0.8325 (tp-100) REVERT: B 73 ARG cc_start: 0.8198 (ttm110) cc_final: 0.7887 (ttm110) REVERT: B 212 ASN cc_start: 0.8132 (t0) cc_final: 0.7639 (t0) REVERT: B 238 ASN cc_start: 0.7697 (m-40) cc_final: 0.7428 (m-40) REVERT: B 296 VAL cc_start: 0.8235 (t) cc_final: 0.7960 (m) REVERT: B 365 ARG cc_start: 0.8393 (ptt90) cc_final: 0.8182 (ptt-90) REVERT: B 469 GLU cc_start: 0.8196 (tt0) cc_final: 0.7949 (tt0) REVERT: C 69 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8549 (ttmm) REVERT: C 89 GLN cc_start: 0.7617 (tp40) cc_final: 0.7065 (pt0) REVERT: C 177 ASP cc_start: 0.8277 (t70) cc_final: 0.8032 (t0) REVERT: C 182 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7698 (mt-10) REVERT: C 212 ASN cc_start: 0.8159 (t0) cc_final: 0.7921 (t0) REVERT: C 278 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8167 (mt) REVERT: C 297 ASP cc_start: 0.7761 (m-30) cc_final: 0.7431 (m-30) REVERT: C 314 SER cc_start: 0.8430 (m) cc_final: 0.8186 (p) REVERT: C 469 GLU cc_start: 0.8198 (tt0) cc_final: 0.7949 (tp30) REVERT: G 28 SER cc_start: 0.8805 (m) cc_final: 0.8424 (p) REVERT: H 28 SER cc_start: 0.8645 (m) cc_final: 0.8331 (p) REVERT: I 28 SER cc_start: 0.8747 (m) cc_final: 0.8384 (p) outliers start: 50 outliers final: 35 residues processed: 433 average time/residue: 0.3046 time to fit residues: 185.9520 Evaluate side-chains 432 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 396 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 399 ASN Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 21 ASP Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.3980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN A 380 ASN B 305 ASN B 380 ASN C 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15450 Z= 0.262 Angle : 0.541 10.937 20919 Z= 0.283 Chirality : 0.044 0.195 2469 Planarity : 0.004 0.045 2673 Dihedral : 5.007 80.948 2136 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.07 % Allowed : 12.77 % Favored : 84.16 % 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: 0.80 (0.19), residues: 1932 helix: 1.40 (0.25), residues: 450 sheet: 0.35 (0.21), residues: 585 loop : 0.36 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 118 HIS 0.001 0.000 HIS A 350 PHE 0.014 0.002 PHE B 427 TYR 0.015 0.002 TYR B 207 ARG 0.007 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 410 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 57 ILE cc_start: 0.8702 (mm) cc_final: 0.8400 (mm) REVERT: A 66 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 70 GLN cc_start: 0.8586 (tp40) cc_final: 0.8311 (tp-100) REVERT: A 73 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7814 (ttm110) REVERT: A 182 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 190 LEU cc_start: 0.9057 (mt) cc_final: 0.8807 (mp) REVERT: A 263 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7966 (mtpt) REVERT: A 331 CYS cc_start: 0.7493 (m) cc_final: 0.7229 (m) REVERT: A 432 GLU cc_start: 0.7503 (mp0) cc_final: 0.7181 (mp0) REVERT: A 459 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7453 (mt-10) REVERT: B 66 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7613 (tp-100) REVERT: B 73 ARG cc_start: 0.8147 (ttm110) cc_final: 0.7845 (ttm110) REVERT: B 212 ASN cc_start: 0.8139 (t0) cc_final: 0.7637 (t0) REVERT: B 238 ASN cc_start: 0.7649 (m-40) cc_final: 0.7371 (m-40) REVERT: B 288 LEU cc_start: 0.7906 (tp) cc_final: 0.7622 (mp) REVERT: B 400 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7476 (ttm-80) REVERT: B 428 ASN cc_start: 0.7845 (t0) cc_final: 0.7562 (t0) REVERT: C 53 LEU cc_start: 0.8723 (mt) cc_final: 0.8447 (mp) REVERT: C 69 LYS cc_start: 0.8800 (ttmm) cc_final: 0.8545 (ttmm) REVERT: C 169 ILE cc_start: 0.8096 (mt) cc_final: 0.7827 (mt) REVERT: C 177 ASP cc_start: 0.8272 (t70) cc_final: 0.8029 (t0) REVERT: C 182 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7672 (mt-10) REVERT: C 212 ASN cc_start: 0.8192 (t0) cc_final: 0.7811 (t0) REVERT: C 297 ASP cc_start: 0.7767 (m-30) cc_final: 0.7430 (m-30) REVERT: C 314 SER cc_start: 0.8436 (m) cc_final: 0.8197 (p) REVERT: C 469 GLU cc_start: 0.8203 (tt0) cc_final: 0.7955 (tp30) REVERT: G 28 SER cc_start: 0.8784 (m) cc_final: 0.8414 (p) REVERT: H 28 SER cc_start: 0.8676 (m) cc_final: 0.8384 (p) REVERT: H 118 TRP cc_start: 0.8443 (m100) cc_final: 0.7964 (m100) REVERT: I 28 SER cc_start: 0.8750 (m) cc_final: 0.8365 (p) outliers start: 52 outliers final: 37 residues processed: 433 average time/residue: 0.3077 time to fit residues: 187.5975 Evaluate side-chains 444 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 406 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 305 ASN A 380 ASN B 70 GLN B 380 ASN C 70 GLN C 305 ASN C 446 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15450 Z= 0.258 Angle : 0.540 10.534 20919 Z= 0.281 Chirality : 0.044 0.174 2469 Planarity : 0.004 0.040 2673 Dihedral : 5.027 79.858 2136 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.43 % Allowed : 13.65 % Favored : 82.92 % 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: 0.73 (0.19), residues: 1932 helix: 1.38 (0.25), residues: 450 sheet: 0.31 (0.21), residues: 585 loop : 0.30 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 118 HIS 0.001 0.000 HIS A 350 PHE 0.015 0.002 PHE B 427 TYR 0.016 0.002 TYR C 338 ARG 0.010 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 417 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 57 ILE cc_start: 0.8707 (mm) cc_final: 0.8419 (mm) REVERT: A 66 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7405 (tm-30) REVERT: A 70 GLN cc_start: 0.8589 (tp40) cc_final: 0.8339 (tp-100) REVERT: A 73 ARG cc_start: 0.8108 (ttm110) cc_final: 0.7778 (ttm110) REVERT: A 182 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7712 (mt-10) REVERT: A 190 LEU cc_start: 0.9068 (mt) cc_final: 0.8785 (mp) REVERT: A 263 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7982 (mtpt) REVERT: A 270 ASP cc_start: 0.7614 (t0) cc_final: 0.7233 (t0) REVERT: A 294 TYR cc_start: 0.8645 (m-80) cc_final: 0.8351 (m-80) REVERT: A 331 CYS cc_start: 0.7499 (m) cc_final: 0.7227 (m) REVERT: A 432 GLU cc_start: 0.7505 (mp0) cc_final: 0.7182 (mp0) REVERT: A 459 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 73 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7837 (ttm110) REVERT: B 169 ILE cc_start: 0.8491 (mt) cc_final: 0.8256 (mt) REVERT: B 212 ASN cc_start: 0.8144 (t0) cc_final: 0.7648 (t0) REVERT: B 238 ASN cc_start: 0.7657 (m-40) cc_final: 0.7389 (m-40) REVERT: B 288 LEU cc_start: 0.7992 (tp) cc_final: 0.7766 (mp) REVERT: B 375 ARG cc_start: 0.8546 (mtt90) cc_final: 0.8274 (mpt90) REVERT: B 400 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7475 (ttm-80) REVERT: B 428 ASN cc_start: 0.7841 (t0) cc_final: 0.7547 (t0) REVERT: C 39 LYS cc_start: 0.8457 (mttt) cc_final: 0.8231 (mtmt) REVERT: C 53 LEU cc_start: 0.8716 (mt) cc_final: 0.8420 (mp) REVERT: C 69 LYS cc_start: 0.8793 (ttmm) cc_final: 0.8546 (ttmm) REVERT: C 169 ILE cc_start: 0.8094 (mt) cc_final: 0.7831 (mt) REVERT: C 177 ASP cc_start: 0.8228 (t70) cc_final: 0.7983 (t0) REVERT: C 182 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7632 (mt-10) REVERT: C 212 ASN cc_start: 0.8176 (t0) cc_final: 0.7952 (t0) REVERT: C 278 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8175 (mt) REVERT: C 297 ASP cc_start: 0.7775 (m-30) cc_final: 0.7426 (m-30) REVERT: C 314 SER cc_start: 0.8439 (m) cc_final: 0.8205 (p) REVERT: C 426 LEU cc_start: 0.8289 (mt) cc_final: 0.8069 (mt) REVERT: C 469 GLU cc_start: 0.8163 (tt0) cc_final: 0.7935 (tp30) REVERT: G 28 SER cc_start: 0.8796 (m) cc_final: 0.8441 (p) REVERT: H 28 SER cc_start: 0.8766 (m) cc_final: 0.8496 (p) REVERT: H 118 TRP cc_start: 0.8459 (m100) cc_final: 0.7915 (m100) REVERT: I 28 SER cc_start: 0.8761 (m) cc_final: 0.8386 (p) outliers start: 58 outliers final: 37 residues processed: 440 average time/residue: 0.3041 time to fit residues: 188.9446 Evaluate side-chains 454 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 415 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 406 ASP Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 305 ASN A 380 ASN B 70 GLN B 380 ASN B 414 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15450 Z= 0.213 Angle : 0.525 9.954 20919 Z= 0.275 Chirality : 0.043 0.162 2469 Planarity : 0.004 0.044 2673 Dihedral : 4.932 78.483 2136 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.01 % Allowed : 14.78 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1932 helix: 1.49 (0.25), residues: 450 sheet: 0.33 (0.21), residues: 588 loop : 0.26 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 118 HIS 0.001 0.000 HIS C 206 PHE 0.012 0.001 PHE C 346 TYR 0.014 0.002 TYR C 338 ARG 0.008 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7687 (mm-30) REVERT: A 57 ILE cc_start: 0.8709 (mm) cc_final: 0.8396 (mm) REVERT: A 66 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7392 (tm-30) REVERT: A 70 GLN cc_start: 0.8582 (tp40) cc_final: 0.8290 (tp-100) REVERT: A 73 ARG cc_start: 0.8092 (ttm110) cc_final: 0.7762 (ttm110) REVERT: A 182 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7703 (mt-10) REVERT: A 190 LEU cc_start: 0.9088 (mt) cc_final: 0.8834 (mp) REVERT: A 263 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7979 (mtpt) REVERT: A 278 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 331 CYS cc_start: 0.7512 (m) cc_final: 0.7233 (m) REVERT: A 432 GLU cc_start: 0.7547 (mp0) cc_final: 0.7230 (mp0) REVERT: A 459 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7451 (mt-10) REVERT: B 73 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7805 (ttm170) REVERT: B 169 ILE cc_start: 0.8450 (mt) cc_final: 0.8204 (mt) REVERT: B 212 ASN cc_start: 0.8140 (t0) cc_final: 0.7639 (t0) REVERT: B 238 ASN cc_start: 0.7638 (m-40) cc_final: 0.7361 (m-40) REVERT: B 288 LEU cc_start: 0.7997 (tp) cc_final: 0.7759 (mp) REVERT: B 375 ARG cc_start: 0.8495 (mtt90) cc_final: 0.8216 (mpt90) REVERT: B 400 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7439 (ttm-80) REVERT: B 428 ASN cc_start: 0.7797 (t0) cc_final: 0.7482 (t0) REVERT: B 459 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7529 (mt-10) REVERT: C 53 LEU cc_start: 0.8718 (mt) cc_final: 0.8413 (mp) REVERT: C 69 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8536 (ttmm) REVERT: C 169 ILE cc_start: 0.8074 (mt) cc_final: 0.7810 (mt) REVERT: C 177 ASP cc_start: 0.8228 (t70) cc_final: 0.7980 (t0) REVERT: C 182 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7618 (mt-10) REVERT: C 204 ASP cc_start: 0.7864 (t0) cc_final: 0.7559 (t0) REVERT: C 212 ASN cc_start: 0.8165 (t0) cc_final: 0.7822 (t0) REVERT: C 278 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8150 (mt) REVERT: C 297 ASP cc_start: 0.7762 (m-30) cc_final: 0.7416 (m-30) REVERT: C 314 SER cc_start: 0.8471 (m) cc_final: 0.8234 (p) REVERT: C 426 LEU cc_start: 0.8266 (mt) cc_final: 0.8049 (mt) REVERT: C 469 GLU cc_start: 0.8167 (tt0) cc_final: 0.7938 (tp30) REVERT: G 28 SER cc_start: 0.8807 (m) cc_final: 0.8467 (p) REVERT: H 28 SER cc_start: 0.8774 (m) cc_final: 0.8524 (p) REVERT: H 118 TRP cc_start: 0.8462 (m100) cc_final: 0.7919 (m100) REVERT: I 28 SER cc_start: 0.8789 (m) cc_final: 0.8423 (p) outliers start: 51 outliers final: 35 residues processed: 424 average time/residue: 0.3072 time to fit residues: 183.5847 Evaluate side-chains 433 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 395 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 117 optimal weight: 0.0770 chunk 126 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 305 ASN A 380 ASN B 70 GLN B 380 ASN C 446 ASN ** F 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15450 Z= 0.194 Angle : 0.522 9.576 20919 Z= 0.271 Chirality : 0.043 0.161 2469 Planarity : 0.004 0.043 2673 Dihedral : 4.850 76.499 2136 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.60 % Allowed : 15.72 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1932 helix: 1.56 (0.25), residues: 459 sheet: 0.37 (0.21), residues: 588 loop : 0.27 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 118 HIS 0.002 0.000 HIS C 206 PHE 0.011 0.001 PHE C 346 TYR 0.016 0.002 TYR C 338 ARG 0.009 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 403 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 57 ILE cc_start: 0.8693 (mm) cc_final: 0.8374 (mm) REVERT: A 70 GLN cc_start: 0.8569 (tp40) cc_final: 0.8270 (tp-100) REVERT: A 73 ARG cc_start: 0.8080 (ttm110) cc_final: 0.7749 (ttm110) REVERT: A 182 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 190 LEU cc_start: 0.9092 (mt) cc_final: 0.8839 (mp) REVERT: A 212 ASN cc_start: 0.8078 (t0) cc_final: 0.7705 (t0) REVERT: A 263 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7988 (mtpt) REVERT: A 278 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 331 CYS cc_start: 0.7512 (m) cc_final: 0.7239 (m) REVERT: A 354 SER cc_start: 0.7863 (m) cc_final: 0.7346 (p) REVERT: A 432 GLU cc_start: 0.7544 (mp0) cc_final: 0.7225 (mp0) REVERT: A 459 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 73 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7763 (ttm170) REVERT: B 92 VAL cc_start: 0.7379 (OUTLIER) cc_final: 0.6995 (p) REVERT: B 169 ILE cc_start: 0.8268 (mt) cc_final: 0.7955 (mt) REVERT: B 212 ASN cc_start: 0.8113 (t0) cc_final: 0.7610 (t0) REVERT: B 237 THR cc_start: 0.8367 (m) cc_final: 0.7849 (p) REVERT: B 238 ASN cc_start: 0.7614 (m-40) cc_final: 0.7387 (t0) REVERT: B 265 ARG cc_start: 0.7578 (ptp-170) cc_final: 0.7377 (ptp-170) REVERT: B 288 LEU cc_start: 0.8005 (tp) cc_final: 0.7764 (mp) REVERT: B 400 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7405 (ttm-80) REVERT: B 428 ASN cc_start: 0.7824 (t0) cc_final: 0.7499 (t0) REVERT: C 53 LEU cc_start: 0.8705 (mt) cc_final: 0.8416 (mp) REVERT: C 69 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8530 (ttmm) REVERT: C 169 ILE cc_start: 0.8042 (mt) cc_final: 0.7792 (mt) REVERT: C 177 ASP cc_start: 0.8273 (t70) cc_final: 0.8040 (t0) REVERT: C 182 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7579 (mt-10) REVERT: C 204 ASP cc_start: 0.7825 (t0) cc_final: 0.7514 (t0) REVERT: C 212 ASN cc_start: 0.8164 (t0) cc_final: 0.7824 (t0) REVERT: C 278 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8141 (mt) REVERT: C 297 ASP cc_start: 0.7776 (m-30) cc_final: 0.7426 (m-30) REVERT: C 314 SER cc_start: 0.8473 (m) cc_final: 0.8235 (p) REVERT: C 426 LEU cc_start: 0.8253 (mt) cc_final: 0.8039 (mt) REVERT: C 469 GLU cc_start: 0.8168 (tt0) cc_final: 0.7941 (tp30) REVERT: D 65 LEU cc_start: 0.8606 (mp) cc_final: 0.8352 (mp) REVERT: G 28 SER cc_start: 0.8803 (m) cc_final: 0.8472 (p) REVERT: H 28 SER cc_start: 0.8789 (m) cc_final: 0.8528 (p) REVERT: H 118 TRP cc_start: 0.8463 (m100) cc_final: 0.7913 (m100) REVERT: I 28 SER cc_start: 0.8789 (m) cc_final: 0.8407 (p) outliers start: 44 outliers final: 34 residues processed: 417 average time/residue: 0.2992 time to fit residues: 175.9792 Evaluate side-chains 431 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 393 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 416 GLU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 0.2980 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 135 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 163 optimal weight: 0.0970 chunk 171 optimal weight: 9.9990 chunk 113 optimal weight: 0.0050 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 302 ASN A 305 ASN A 380 ASN B 70 GLN B 380 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15450 Z= 0.160 Angle : 0.511 9.341 20919 Z= 0.264 Chirality : 0.043 0.156 2469 Planarity : 0.003 0.044 2673 Dihedral : 4.680 72.920 2136 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.30 % Allowed : 16.78 % Favored : 80.91 % 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: 0.90 (0.19), residues: 1932 helix: 1.63 (0.25), residues: 459 sheet: 0.46 (0.22), residues: 558 loop : 0.28 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 118 HIS 0.002 0.001 HIS C 206 PHE 0.011 0.001 PHE C 346 TYR 0.014 0.001 TYR C 338 ARG 0.010 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 405 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8300 (mtpp) REVERT: A 45 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7756 (mm-30) REVERT: A 57 ILE cc_start: 0.8705 (mm) cc_final: 0.8388 (mm) REVERT: A 70 GLN cc_start: 0.8529 (tp40) cc_final: 0.7956 (tp40) REVERT: A 73 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7706 (ttm110) REVERT: A 169 ILE cc_start: 0.8461 (mt) cc_final: 0.8236 (mt) REVERT: A 182 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7671 (mt-10) REVERT: A 186 CYS cc_start: 0.7548 (p) cc_final: 0.7241 (p) REVERT: A 190 LEU cc_start: 0.9056 (mt) cc_final: 0.8850 (mp) REVERT: A 212 ASN cc_start: 0.8067 (t0) cc_final: 0.7734 (t0) REVERT: A 263 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7989 (mtpt) REVERT: A 278 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8100 (mt) REVERT: A 294 TYR cc_start: 0.8573 (m-80) cc_final: 0.8323 (m-80) REVERT: A 331 CYS cc_start: 0.7522 (m) cc_final: 0.7246 (m) REVERT: A 431 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7725 (mmtt) REVERT: A 432 GLU cc_start: 0.7532 (mp0) cc_final: 0.7216 (mp0) REVERT: A 459 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7435 (mt-10) REVERT: B 76 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: B 92 VAL cc_start: 0.7261 (OUTLIER) cc_final: 0.6811 (p) REVERT: B 169 ILE cc_start: 0.8167 (mt) cc_final: 0.7830 (mt) REVERT: B 212 ASN cc_start: 0.8115 (t0) cc_final: 0.7608 (t0) REVERT: B 238 ASN cc_start: 0.7611 (m-40) cc_final: 0.7317 (t0) REVERT: B 296 VAL cc_start: 0.8252 (t) cc_final: 0.7991 (m) REVERT: B 400 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7374 (ttm-80) REVERT: B 428 ASN cc_start: 0.7786 (t0) cc_final: 0.7445 (t0) REVERT: C 53 LEU cc_start: 0.8714 (mt) cc_final: 0.8429 (mp) REVERT: C 69 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8518 (ttmm) REVERT: C 169 ILE cc_start: 0.7992 (mt) cc_final: 0.7722 (mt) REVERT: C 177 ASP cc_start: 0.8244 (t70) cc_final: 0.8005 (t0) REVERT: C 182 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 204 ASP cc_start: 0.7781 (t0) cc_final: 0.7491 (t0) REVERT: C 260 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7570 (mm-30) REVERT: C 297 ASP cc_start: 0.7798 (m-30) cc_final: 0.7468 (m-30) REVERT: C 314 SER cc_start: 0.8485 (m) cc_final: 0.8252 (p) REVERT: C 426 LEU cc_start: 0.8243 (mt) cc_final: 0.8021 (mt) REVERT: C 469 GLU cc_start: 0.8172 (tt0) cc_final: 0.7939 (tp30) REVERT: D 65 LEU cc_start: 0.8618 (mp) cc_final: 0.8352 (mp) REVERT: G 28 SER cc_start: 0.8818 (m) cc_final: 0.8485 (p) REVERT: H 28 SER cc_start: 0.8760 (m) cc_final: 0.8500 (p) REVERT: H 118 TRP cc_start: 0.8466 (m100) cc_final: 0.7963 (m100) REVERT: I 28 SER cc_start: 0.8789 (m) cc_final: 0.8412 (p) outliers start: 39 outliers final: 26 residues processed: 414 average time/residue: 0.3273 time to fit residues: 192.8205 Evaluate side-chains 427 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 397 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 399 ASN Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 10.0000 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 0.3980 chunk 191 optimal weight: 0.4980 chunk 176 optimal weight: 10.0000 chunk 152 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 0.0870 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 ASN A 380 ASN B 70 GLN B 380 ASN C 380 ASN C 446 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15450 Z= 0.153 Angle : 0.516 9.397 20919 Z= 0.264 Chirality : 0.042 0.144 2469 Planarity : 0.003 0.054 2673 Dihedral : 4.571 69.094 2136 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.65 % Allowed : 18.09 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.20), residues: 1932 helix: 1.61 (0.25), residues: 465 sheet: 0.42 (0.21), residues: 597 loop : 0.33 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 118 HIS 0.003 0.001 HIS A 206 PHE 0.010 0.001 PHE C 346 TYR 0.020 0.001 TYR A 207 ARG 0.009 0.000 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 396 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 45 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7737 (mm-30) REVERT: A 57 ILE cc_start: 0.8696 (mm) cc_final: 0.8365 (mm) REVERT: A 70 GLN cc_start: 0.8544 (tp40) cc_final: 0.7967 (tp40) REVERT: A 73 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7661 (ttm110) REVERT: A 182 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7652 (mt-10) REVERT: A 263 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7988 (mtpt) REVERT: A 278 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8073 (mt) REVERT: A 294 TYR cc_start: 0.8584 (m-80) cc_final: 0.8292 (m-80) REVERT: A 354 SER cc_start: 0.7806 (m) cc_final: 0.7256 (p) REVERT: A 431 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7717 (mmtt) REVERT: A 432 GLU cc_start: 0.7539 (mp0) cc_final: 0.7219 (mp0) REVERT: B 92 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6865 (m) REVERT: B 169 ILE cc_start: 0.8125 (mt) cc_final: 0.7781 (mt) REVERT: B 212 ASN cc_start: 0.8112 (t0) cc_final: 0.7601 (t0) REVERT: B 238 ASN cc_start: 0.7572 (m-40) cc_final: 0.7172 (t0) REVERT: B 281 ARG cc_start: 0.7930 (mtm-85) cc_final: 0.7724 (mtm-85) REVERT: B 296 VAL cc_start: 0.8255 (t) cc_final: 0.8006 (m) REVERT: B 400 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7361 (ttm-80) REVERT: B 428 ASN cc_start: 0.7792 (t0) cc_final: 0.7455 (t0) REVERT: C 39 LYS cc_start: 0.8304 (mttt) cc_final: 0.8043 (mtmt) REVERT: C 53 LEU cc_start: 0.8720 (mt) cc_final: 0.8439 (mp) REVERT: C 69 LYS cc_start: 0.8726 (ttmm) cc_final: 0.8474 (ttmm) REVERT: C 169 ILE cc_start: 0.8025 (mt) cc_final: 0.7765 (mt) REVERT: C 177 ASP cc_start: 0.8251 (t70) cc_final: 0.7984 (t0) REVERT: C 182 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 204 ASP cc_start: 0.7797 (t0) cc_final: 0.7486 (t0) REVERT: C 260 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7554 (mm-30) REVERT: C 297 ASP cc_start: 0.7807 (m-30) cc_final: 0.7460 (m-30) REVERT: C 314 SER cc_start: 0.8486 (m) cc_final: 0.8250 (p) REVERT: C 426 LEU cc_start: 0.8241 (mt) cc_final: 0.8019 (mt) REVERT: C 469 GLU cc_start: 0.8172 (tt0) cc_final: 0.7938 (tp30) REVERT: D 65 LEU cc_start: 0.8618 (mp) cc_final: 0.8350 (mp) REVERT: G 28 SER cc_start: 0.8816 (m) cc_final: 0.8478 (p) REVERT: H 28 SER cc_start: 0.8742 (m) cc_final: 0.8505 (p) REVERT: H 118 TRP cc_start: 0.8463 (m100) cc_final: 0.7955 (m100) REVERT: I 28 SER cc_start: 0.8790 (m) cc_final: 0.8418 (p) outliers start: 28 outliers final: 22 residues processed: 405 average time/residue: 0.3323 time to fit residues: 191.5030 Evaluate side-chains 421 residues out of total 1692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 396 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 276 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 227 LYS Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain H residue 58 SER Chi-restraints excluded: chain H residue 91 MET Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 140 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 305 ASN A 380 ASN B 380 ASN C 380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.134519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109000 restraints weight = 22390.990| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.46 r_work: 0.3150 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15450 Z= 0.176 Angle : 0.524 9.300 20919 Z= 0.269 Chirality : 0.043 0.144 2469 Planarity : 0.004 0.057 2673 Dihedral : 4.473 64.344 2136 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.60 % Allowed : 18.85 % Favored : 79.55 % 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: 0.90 (0.20), residues: 1932 helix: 1.59 (0.25), residues: 465 sheet: 0.48 (0.22), residues: 567 loop : 0.28 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 118 HIS 0.002 0.000 HIS C 206 PHE 0.011 0.001 PHE C 346 TYR 0.020 0.002 TYR A 71 ARG 0.007 0.000 ARG B 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4249.19 seconds wall clock time: 75 minutes 40.90 seconds (4540.90 seconds total)