Starting phenix.real_space_refine on Thu Feb 5 02:28:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.map" model { file = "/net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pky_71707/02_2026/9pky_71707.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 89 5.16 5 C 9389 2.51 5 N 2255 2.21 5 O 2568 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14301 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2774 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 15, 'TRANS': 326} Chain breaks: 1 Chain: "D" Number of atoms: 2755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2755 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "C" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2766 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2818 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2669 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'IVM': 2, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'IVM': 1, 'NAG': 1, 'SY9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.08, per 1000 atoms: 0.22 Number of scatterers: 14301 At special positions: 0 Unit cell: (93.24, 93.24, 135.24, 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 89 16.00 O 2568 8.00 N 2255 7.00 C 9389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 182 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS E 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 62 " " NAG B 502 " - " ASN B 62 " " NAG C 503 " - " ASN C 62 " " NAG D 501 " - " ASN D 62 " " NAG E 601 " - " ASN E 54 " " NAG E 602 " - " ASN E 241 " Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 427.2 milliseconds 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 22 sheets defined 40.5% alpha, 38.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.501A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 110 through 117 removed outlier: 3.551A pdb=" N LEU A 114 " --> pdb=" O PRO A 111 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP A 115 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 117 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.560A pdb=" N VAL A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 272 through 295 removed outlier: 4.172A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 335 removed outlier: 3.637A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 439 removed outlier: 3.637A pdb=" N ASP A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 110 through 117 removed outlier: 3.634A pdb=" N LEU D 114 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASP D 115 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 117 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 264 through 268 Processing helix chain 'D' and resid 272 through 294 Processing helix chain 'D' and resid 305 through 333 removed outlier: 3.816A pdb=" N ARG D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 439 removed outlier: 3.813A pdb=" N VAL D 416 " --> pdb=" O THR D 412 " (cutoff:3.500A) Proline residue: D 419 - end of helix removed outlier: 3.674A pdb=" N ILE D 436 " --> pdb=" O THR D 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 Processing helix chain 'C' and resid 95 through 98 Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.695A pdb=" N LEU C 114 " --> pdb=" O PRO C 111 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP C 115 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE C 117 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.652A pdb=" N LEU C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 272 through 294 removed outlier: 3.633A pdb=" N THR C 283 " --> pdb=" O LEU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 337 removed outlier: 3.740A pdb=" N GLN C 334 " --> pdb=" O PHE C 330 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS C 335 " --> pdb=" O ILE C 331 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS C 336 " --> pdb=" O ALA C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 435 removed outlier: 3.571A pdb=" N ASP C 411 " --> pdb=" O ALA C 407 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 416 " --> pdb=" O THR C 412 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.548A pdb=" N ALA B 98 " --> pdb=" O PRO B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 110 through 117 removed outlier: 3.675A pdb=" N LEU B 114 " --> pdb=" O PRO B 111 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP B 115 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.512A pdb=" N LEU B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.581A pdb=" N SER B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 272 through 293 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 305 through 334 removed outlier: 3.512A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 333 " --> pdb=" O ASN B 329 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 439 removed outlier: 3.529A pdb=" N ASP B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 416 " --> pdb=" O THR B 412 " (cutoff:3.500A) Proline residue: B 419 - end of helix removed outlier: 3.601A pdb=" N ILE B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 436 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG B 437 " --> pdb=" O TYR B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 444 Processing helix chain 'E' and resid 55 through 63 removed outlier: 3.504A pdb=" N LEU E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 removed outlier: 4.492A pdb=" N LYS E 135 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 191 Processing helix chain 'E' and resid 265 through 272 Processing helix chain 'E' and resid 272 through 285 removed outlier: 3.590A pdb=" N LEU E 285 " --> pdb=" O VAL E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 289 Processing helix chain 'E' and resid 293 through 316 removed outlier: 3.547A pdb=" N ARG E 297 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Proline residue: E 299 - end of helix removed outlier: 3.620A pdb=" N SER E 304 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 326 through 352 removed outlier: 3.819A pdb=" N ALA E 334 " --> pdb=" O ILE E 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 343 " --> pdb=" O GLY E 339 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 476 removed outlier: 3.520A pdb=" N ASP E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.243A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.629A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA6, first strand: chain 'D' and resid 106 through 108 removed outlier: 4.530A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.483A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 122 through 124 removed outlier: 3.516A pdb=" N GLU D 235 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N HIS D 239 " --> pdb=" O GLU D 216 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU D 216 " --> pdb=" O HIS D 239 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N GLU D 241 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LYS D 214 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108 removed outlier: 4.531A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.389A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 removed outlier: 4.949A pdb=" N HIS C 239 " --> pdb=" O GLU C 216 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU C 216 " --> pdb=" O HIS C 239 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N GLU C 241 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS C 214 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AB5, first strand: chain 'B' and resid 106 through 108 removed outlier: 4.561A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.536A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB8, first strand: chain 'B' and resid 122 through 124 Processing sheet with id=AB9, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AC1, first strand: chain 'E' and resid 126 through 128 removed outlier: 4.530A pdb=" N ASP E 169 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL E 80 " --> pdb=" O GLN E 211 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N MET E 213 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ASP E 82 " --> pdb=" O MET E 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 147 through 150 removed outlier: 6.467A pdb=" N THR E 179 " --> pdb=" O LYS E 148 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA E 150 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER E 177 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP E 100 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N SER E 93 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG E 102 " --> pdb=" O PHE E 91 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE E 91 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN E 104 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN E 112 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU E 81 " --> pdb=" O ASN E 112 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 142 through 144 removed outlier: 3.765A pdb=" N CYS E 196 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE E 259 " --> pdb=" O CYS E 196 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 244 through 245 785 hydrogen bonds defined for protein. 2247 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: 2.58 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2756 1.33 - 1.45: 3658 1.45 - 1.57: 8149 1.57 - 1.69: 0 1.69 - 1.82: 147 Bond restraints: 14710 Sorted by residual: bond pdb=" N ASN D 131 " pdb=" CA ASN D 131 " ideal model delta sigma weight residual 1.456 1.491 -0.034 1.16e-02 7.43e+03 8.82e+00 bond pdb=" N VAL D 135 " pdb=" CA VAL D 135 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.63e+00 bond pdb=" N LYS D 140 " pdb=" CA LYS D 140 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.26e-02 6.30e+03 6.89e+00 bond pdb=" C1 NAG B 502 " pdb=" O5 NAG B 502 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" N LEU D 141 " pdb=" CA LEU D 141 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.20e-02 6.94e+03 6.51e+00 ... (remaining 14705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 19127 1.49 - 2.98: 705 2.98 - 4.46: 157 4.46 - 5.95: 58 5.95 - 7.44: 8 Bond angle restraints: 20055 Sorted by residual: angle pdb=" N VAL D 416 " pdb=" CA VAL D 416 " pdb=" C VAL D 416 " ideal model delta sigma weight residual 111.90 109.31 2.59 8.10e-01 1.52e+00 1.02e+01 angle pdb=" CA ASN D 139 " pdb=" C ASN D 139 " pdb=" O ASN D 139 " ideal model delta sigma weight residual 122.44 118.28 4.16 1.34e+00 5.57e-01 9.63e+00 angle pdb=" CA ASN D 131 " pdb=" C ASN D 131 " pdb=" O ASN D 131 " ideal model delta sigma weight residual 121.38 118.22 3.16 1.06e+00 8.90e-01 8.90e+00 angle pdb=" CA GLU D 134 " pdb=" C GLU D 134 " pdb=" O GLU D 134 " ideal model delta sigma weight residual 122.31 118.45 3.86 1.31e+00 5.83e-01 8.68e+00 angle pdb=" CA ASP D 138 " pdb=" CB ASP D 138 " pdb=" CG ASP D 138 " ideal model delta sigma weight residual 112.60 115.52 -2.92 1.00e+00 1.00e+00 8.54e+00 ... (remaining 20050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.46: 8914 24.46 - 48.92: 471 48.92 - 73.38: 110 73.38 - 97.84: 22 97.84 - 122.30: 26 Dihedral angle restraints: 9543 sinusoidal: 4520 harmonic: 5023 Sorted by residual: dihedral pdb=" CA CYS E 196 " pdb=" C CYS E 196 " pdb=" N LYS E 197 " pdb=" CA LYS E 197 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLU E 256 " pdb=" C GLU E 256 " pdb=" N VAL E 257 " pdb=" CA VAL E 257 " ideal model delta harmonic sigma weight residual 180.00 156.94 23.06 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA PHE D 169 " pdb=" C PHE D 169 " pdb=" N PRO D 170 " pdb=" CA PRO D 170 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 9540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1969 0.069 - 0.138: 305 0.138 - 0.207: 30 0.207 - 0.275: 13 0.275 - 0.344: 2 Chirality restraints: 2319 Sorted by residual: chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 54 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.96e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 62 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C34 IVM D 503 " pdb=" C19 IVM D 503 " pdb=" C35 IVM D 503 " pdb=" C36 IVM D 503 " both_signs ideal model delta sigma weight residual False -2.51 -2.75 0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2316 not shown) Planarity restraints: 2439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C37 IVM C 502 " -0.375 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C38 IVM C 502 " 0.509 2.00e-02 2.50e+03 pdb=" C39 IVM C 502 " 0.150 2.00e-02 2.50e+03 pdb=" C40 IVM C 502 " -0.154 2.00e-02 2.50e+03 pdb=" C47 IVM C 502 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C37 IVM A 504 " -0.328 2.00e-02 2.50e+03 2.71e-01 9.21e+02 pdb=" C38 IVM A 504 " 0.486 2.00e-02 2.50e+03 pdb=" C39 IVM A 504 " 0.050 2.00e-02 2.50e+03 pdb=" C40 IVM A 504 " -0.111 2.00e-02 2.50e+03 pdb=" C47 IVM A 504 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C34 IVM B 501 " 0.094 2.00e-02 2.50e+03 2.55e-01 6.50e+02 pdb=" C36 IVM B 501 " -0.331 2.00e-02 2.50e+03 pdb=" C37 IVM B 501 " 0.357 2.00e-02 2.50e+03 pdb=" C38 IVM B 501 " -0.119 2.00e-02 2.50e+03 ... (remaining 2436 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2620 2.77 - 3.30: 13080 3.30 - 3.84: 23152 3.84 - 4.37: 28296 4.37 - 4.90: 48338 Nonbonded interactions: 115486 Sorted by model distance: nonbonded pdb=" O PRO D 60 " pdb=" O3 NAG D 501 " model vdw 2.240 3.040 nonbonded pdb=" O ALA C 332 " pdb=" ND1 HIS C 335 " model vdw 2.245 3.120 nonbonded pdb=" OE1 GLU C 193 " pdb=" OH TYR C 221 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.271 3.040 nonbonded pdb=" O LEU A 285 " pdb=" OG1 THR A 288 " model vdw 2.283 3.040 ... (remaining 115481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 333 or resid 401 through 436)) selection = (chain 'B' and (resid 33 through 333 or resid 401 through 436)) selection = (chain 'C' and (resid 33 through 333 or resid 336 or resid 402 through 436)) selection = (chain 'D' and resid 33 through 436) } 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: 1.970 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.000 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 : 0.004 0.052 14718 Z= 0.204 Angle : 0.752 18.618 20077 Z= 0.352 Chirality : 0.052 0.344 2319 Planarity : 0.015 0.304 2433 Dihedral : 16.918 122.298 6277 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.20), residues: 1678 helix: -0.05 (0.21), residues: 559 sheet: 0.62 (0.28), residues: 397 loop : -0.28 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 83 TYR 0.016 0.001 TYR D 102 PHE 0.012 0.001 PHE C 403 TRP 0.036 0.001 TRP E 284 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00416 (14710) covalent geometry : angle 0.71447 (20055) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.36831 ( 4) hydrogen bonds : bond 0.25394 ( 670) hydrogen bonds : angle 7.41780 ( 2247) link_NAG-ASN : bond 0.01425 ( 6) link_NAG-ASN : angle 7.79641 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.439 Fit side-chains REVERT: C 244 MET cc_start: 0.8248 (tpp) cc_final: 0.8034 (mmm) REVERT: E 122 PHE cc_start: 0.7646 (t80) cc_final: 0.7444 (t80) REVERT: E 136 CYS cc_start: 0.8639 (m) cc_final: 0.8365 (m) REVERT: E 151 ASN cc_start: 0.8256 (m110) cc_final: 0.7962 (m110) REVERT: E 468 LYS cc_start: 0.7142 (pttm) cc_final: 0.6490 (mptt) REVERT: E 473 TYR cc_start: 0.7592 (t80) cc_final: 0.7385 (t80) outliers start: 0 outliers final: 1 residues processed: 210 average time/residue: 0.6225 time to fit residues: 142.3031 Evaluate side-chains 154 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 302 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 139 ASN C 243 GLN B 66 ASN E 95 GLN E 157 GLN E 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.100146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.078111 restraints weight = 26452.822| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.86 r_work: 0.2932 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14718 Z= 0.144 Angle : 0.717 15.465 20077 Z= 0.334 Chirality : 0.046 0.337 2319 Planarity : 0.004 0.049 2433 Dihedral : 10.242 90.860 2974 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.64 % Allowed : 10.46 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1678 helix: 1.49 (0.21), residues: 568 sheet: 0.81 (0.28), residues: 379 loop : -0.27 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 83 TYR 0.021 0.001 TYR D 325 PHE 0.016 0.001 PHE D 132 TRP 0.018 0.001 TRP E 284 HIS 0.003 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00306 (14710) covalent geometry : angle 0.68862 (20055) SS BOND : bond 0.00132 ( 2) SS BOND : angle 1.15297 ( 4) hydrogen bonds : bond 0.05576 ( 670) hydrogen bonds : angle 4.48629 ( 2247) link_NAG-ASN : bond 0.01176 ( 6) link_NAG-ASN : angle 6.64478 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: A 42 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7723 (mtp) REVERT: A 333 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7867 (tmm160) REVERT: A 334 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 408 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8102 (pttm) REVERT: E 122 PHE cc_start: 0.7687 (t80) cc_final: 0.7328 (t80) REVERT: E 136 CYS cc_start: 0.9280 (m) cc_final: 0.8842 (m) REVERT: E 151 ASN cc_start: 0.8668 (m110) cc_final: 0.8317 (m110) REVERT: E 269 MET cc_start: 0.8830 (tpp) cc_final: 0.8585 (tpp) REVERT: E 284 TRP cc_start: 0.8437 (m-10) cc_final: 0.8010 (m-10) REVERT: E 468 LYS cc_start: 0.6821 (pttm) cc_final: 0.6281 (pmtt) REVERT: E 473 TYR cc_start: 0.7647 (t80) cc_final: 0.7255 (t80) outliers start: 25 outliers final: 8 residues processed: 189 average time/residue: 0.5731 time to fit residues: 118.9867 Evaluate side-chains 171 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 162 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 290 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 75 optimal weight: 0.0010 chunk 137 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 93 ASN D 149 ASN C 243 GLN E 95 GLN E 157 GLN E 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.096272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.073922 restraints weight = 27061.099| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.86 r_work: 0.2853 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14718 Z= 0.250 Angle : 0.730 15.893 20077 Z= 0.348 Chirality : 0.048 0.326 2319 Planarity : 0.004 0.038 2433 Dihedral : 8.417 58.281 2972 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.75 % Allowed : 13.15 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.21), residues: 1678 helix: 1.68 (0.21), residues: 574 sheet: 0.63 (0.27), residues: 395 loop : -0.29 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.025 0.002 TYR D 325 PHE 0.023 0.002 PHE D 132 TRP 0.017 0.001 TRP E 284 HIS 0.004 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00593 (14710) covalent geometry : angle 0.69938 (20055) SS BOND : bond 0.00071 ( 2) SS BOND : angle 1.97185 ( 4) hydrogen bonds : bond 0.05713 ( 670) hydrogen bonds : angle 4.36116 ( 2247) link_NAG-ASN : bond 0.01100 ( 6) link_NAG-ASN : angle 6.92787 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.593 Fit side-chains REVERT: A 42 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7792 (mtp) REVERT: A 83 ARG cc_start: 0.9006 (ttm-80) cc_final: 0.8771 (ttt-90) REVERT: A 334 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7685 (tm-30) REVERT: D 438 SER cc_start: 0.8728 (m) cc_final: 0.8520 (p) REVERT: B 83 ARG cc_start: 0.8887 (ttp-110) cc_final: 0.8619 (ttm110) REVERT: B 408 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8092 (pttm) REVERT: E 122 PHE cc_start: 0.7831 (t80) cc_final: 0.7489 (t80) REVERT: E 132 LYS cc_start: 0.8486 (tptt) cc_final: 0.8248 (tptt) REVERT: E 135 LYS cc_start: 0.9379 (pttp) cc_final: 0.9163 (pttm) REVERT: E 136 CYS cc_start: 0.9289 (m) cc_final: 0.8795 (m) REVERT: E 269 MET cc_start: 0.8810 (OUTLIER) cc_final: 0.8581 (tpp) REVERT: E 468 LYS cc_start: 0.7001 (pttm) cc_final: 0.6778 (pttm) REVERT: E 473 TYR cc_start: 0.7613 (t80) cc_final: 0.7280 (t80) outliers start: 42 outliers final: 20 residues processed: 182 average time/residue: 0.6243 time to fit residues: 124.5742 Evaluate side-chains 175 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 251 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 428 PHE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 14 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 243 GLN E 95 GLN E 157 GLN E 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.099366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.077221 restraints weight = 26711.557| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.85 r_work: 0.2914 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14718 Z= 0.126 Angle : 0.629 15.485 20077 Z= 0.296 Chirality : 0.044 0.332 2319 Planarity : 0.004 0.040 2433 Dihedral : 7.294 58.999 2972 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.94 % Allowed : 14.13 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1678 helix: 2.02 (0.21), residues: 576 sheet: 0.76 (0.27), residues: 401 loop : -0.23 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 117 TYR 0.022 0.001 TYR D 325 PHE 0.013 0.001 PHE E 340 TRP 0.013 0.001 TRP E 284 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00282 (14710) covalent geometry : angle 0.59632 (20055) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.05309 ( 4) hydrogen bonds : bond 0.04225 ( 670) hydrogen bonds : angle 3.97608 ( 2247) link_NAG-ASN : bond 0.01282 ( 6) link_NAG-ASN : angle 6.69723 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.565 Fit side-chains REVERT: A 83 ARG cc_start: 0.8973 (ttm-80) cc_final: 0.8757 (ttt-90) REVERT: A 333 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7752 (tmm160) REVERT: D 438 SER cc_start: 0.8714 (m) cc_final: 0.8504 (p) REVERT: B 83 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8598 (ttm110) REVERT: B 134 GLU cc_start: 0.7986 (pm20) cc_final: 0.7607 (tp30) REVERT: B 408 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8065 (pttm) REVERT: E 122 PHE cc_start: 0.7695 (t80) cc_final: 0.7432 (t80) REVERT: E 136 CYS cc_start: 0.9307 (m) cc_final: 0.8830 (m) REVERT: E 284 TRP cc_start: 0.8426 (m-10) cc_final: 0.8093 (m-10) REVERT: E 468 LYS cc_start: 0.6985 (pttm) cc_final: 0.6762 (pttm) REVERT: E 473 TYR cc_start: 0.7450 (t80) cc_final: 0.7065 (t80) outliers start: 45 outliers final: 16 residues processed: 191 average time/residue: 0.6008 time to fit residues: 126.0863 Evaluate side-chains 174 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 332 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 139 ASN C 243 GLN B 168 ASN E 95 GLN E 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075465 restraints weight = 26826.963| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.82 r_work: 0.2882 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14718 Z= 0.175 Angle : 0.652 15.478 20077 Z= 0.310 Chirality : 0.046 0.330 2319 Planarity : 0.004 0.040 2433 Dihedral : 7.160 58.067 2972 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 15.24 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1678 helix: 2.00 (0.21), residues: 577 sheet: 0.75 (0.28), residues: 390 loop : -0.22 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.024 0.001 TYR D 325 PHE 0.015 0.001 PHE D 132 TRP 0.016 0.001 TRP B 263 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00411 (14710) covalent geometry : angle 0.61934 (20055) SS BOND : bond 0.00087 ( 2) SS BOND : angle 1.44184 ( 4) hydrogen bonds : bond 0.04543 ( 670) hydrogen bonds : angle 3.97880 ( 2247) link_NAG-ASN : bond 0.01182 ( 6) link_NAG-ASN : angle 6.79939 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 162 time to evaluate : 0.568 Fit side-chains REVERT: A 333 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7330 (ttm170) REVERT: D 438 SER cc_start: 0.8676 (m) cc_final: 0.8454 (p) REVERT: C 404 ILE cc_start: 0.8421 (mp) cc_final: 0.8070 (mp) REVERT: B 83 ARG cc_start: 0.8871 (ttp-110) cc_final: 0.8605 (ttm110) REVERT: B 134 GLU cc_start: 0.8016 (pm20) cc_final: 0.7560 (tp30) REVERT: B 408 LYS cc_start: 0.8366 (ttpt) cc_final: 0.8084 (pttm) REVERT: E 122 PHE cc_start: 0.7734 (t80) cc_final: 0.7502 (t80) REVERT: E 136 CYS cc_start: 0.9286 (m) cc_final: 0.8823 (m) REVERT: E 473 TYR cc_start: 0.7465 (t80) cc_final: 0.7114 (t80) outliers start: 50 outliers final: 26 residues processed: 187 average time/residue: 0.5702 time to fit residues: 117.5025 Evaluate side-chains 174 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 122 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 140 optimal weight: 0.0020 chunk 18 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 243 GLN B 335 HIS E 95 GLN E 157 GLN E 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.100039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.077989 restraints weight = 26659.372| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.85 r_work: 0.2934 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14718 Z= 0.111 Angle : 0.612 15.197 20077 Z= 0.288 Chirality : 0.044 0.332 2319 Planarity : 0.004 0.041 2433 Dihedral : 6.622 55.308 2972 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.62 % Allowed : 16.48 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.21), residues: 1678 helix: 2.14 (0.21), residues: 574 sheet: 0.86 (0.27), residues: 400 loop : -0.21 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.021 0.001 TYR D 325 PHE 0.017 0.001 PHE B 319 TRP 0.017 0.001 TRP B 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00244 (14710) covalent geometry : angle 0.58008 (20055) SS BOND : bond 0.00131 ( 2) SS BOND : angle 0.89830 ( 4) hydrogen bonds : bond 0.03891 ( 670) hydrogen bonds : angle 3.79204 ( 2247) link_NAG-ASN : bond 0.01283 ( 6) link_NAG-ASN : angle 6.57371 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.595 Fit side-chains revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.7188 (ttm170) REVERT: D 438 SER cc_start: 0.8697 (m) cc_final: 0.8469 (p) REVERT: C 248 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9056 (mp) REVERT: C 404 ILE cc_start: 0.8375 (mp) cc_final: 0.8024 (mp) REVERT: B 83 ARG cc_start: 0.8866 (ttp-110) cc_final: 0.8589 (ttm110) REVERT: B 134 GLU cc_start: 0.7871 (pm20) cc_final: 0.7518 (tp30) REVERT: B 333 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7223 (mtm-85) REVERT: B 408 LYS cc_start: 0.8316 (ttpt) cc_final: 0.8046 (pttm) REVERT: E 132 LYS cc_start: 0.8367 (tptt) cc_final: 0.8135 (tptt) REVERT: E 136 CYS cc_start: 0.9285 (m) cc_final: 0.8819 (m) REVERT: E 197 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8604 (ptpt) REVERT: E 284 TRP cc_start: 0.8455 (m-10) cc_final: 0.8041 (m-10) outliers start: 40 outliers final: 23 residues processed: 190 average time/residue: 0.5307 time to fit residues: 111.7321 Evaluate side-chains 186 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 197 LYS Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 0.3980 chunk 133 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN C 290 GLN B 168 ASN B 335 HIS E 95 GLN E 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.099377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.077399 restraints weight = 26557.251| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.83 r_work: 0.2925 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14718 Z= 0.128 Angle : 0.621 14.947 20077 Z= 0.294 Chirality : 0.044 0.331 2319 Planarity : 0.004 0.042 2433 Dihedral : 6.551 57.819 2972 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.62 % Allowed : 17.00 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.21), residues: 1678 helix: 2.11 (0.21), residues: 578 sheet: 0.90 (0.27), residues: 400 loop : -0.19 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 83 TYR 0.023 0.001 TYR D 325 PHE 0.012 0.001 PHE E 340 TRP 0.025 0.001 TRP B 263 HIS 0.003 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00295 (14710) covalent geometry : angle 0.58943 (20055) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.09769 ( 4) hydrogen bonds : bond 0.03957 ( 670) hydrogen bonds : angle 3.78017 ( 2247) link_NAG-ASN : bond 0.01206 ( 6) link_NAG-ASN : angle 6.52981 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 333 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7226 (ttm170) REVERT: D 438 SER cc_start: 0.8681 (m) cc_final: 0.8461 (p) REVERT: C 248 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9117 (mp) REVERT: C 404 ILE cc_start: 0.8390 (mp) cc_final: 0.7985 (mp) REVERT: B 83 ARG cc_start: 0.8885 (ttp-110) cc_final: 0.8616 (ttm110) REVERT: B 134 GLU cc_start: 0.7871 (pm20) cc_final: 0.7544 (tp30) REVERT: B 408 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8099 (pttm) REVERT: E 136 CYS cc_start: 0.9282 (m) cc_final: 0.8831 (m) REVERT: E 284 TRP cc_start: 0.8552 (m-10) cc_final: 0.8007 (m-10) outliers start: 40 outliers final: 25 residues processed: 190 average time/residue: 0.5335 time to fit residues: 112.0829 Evaluate side-chains 183 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 18 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN B 335 HIS E 95 GLN E 157 GLN E 290 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.074438 restraints weight = 26770.472| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.84 r_work: 0.2859 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14718 Z= 0.226 Angle : 0.694 15.232 20077 Z= 0.331 Chirality : 0.047 0.334 2319 Planarity : 0.004 0.042 2433 Dihedral : 6.954 59.746 2972 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 17.14 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.21), residues: 1678 helix: 1.93 (0.21), residues: 578 sheet: 0.68 (0.28), residues: 397 loop : -0.25 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 83 TYR 0.025 0.002 TYR D 325 PHE 0.018 0.002 PHE C 123 TRP 0.039 0.002 TRP B 263 HIS 0.005 0.001 HIS C 133 Details of bonding type rmsd covalent geometry : bond 0.00538 (14710) covalent geometry : angle 0.66415 (20055) SS BOND : bond 0.00103 ( 2) SS BOND : angle 1.63670 ( 4) hydrogen bonds : bond 0.04717 ( 670) hydrogen bonds : angle 4.01400 ( 2247) link_NAG-ASN : bond 0.01103 ( 6) link_NAG-ASN : angle 6.77590 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.469 Fit side-chains REVERT: A 83 ARG cc_start: 0.9034 (ttt90) cc_final: 0.8750 (ttt-90) REVERT: D 438 SER cc_start: 0.8672 (m) cc_final: 0.8459 (p) REVERT: C 248 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9156 (mp) REVERT: B 77 GLU cc_start: 0.8336 (mp0) cc_final: 0.8062 (mp0) REVERT: B 83 ARG cc_start: 0.8897 (ttp-110) cc_final: 0.8606 (ttm110) REVERT: B 134 GLU cc_start: 0.8086 (pm20) cc_final: 0.7570 (tp30) REVERT: B 408 LYS cc_start: 0.8385 (ttpt) cc_final: 0.8115 (pttm) REVERT: E 136 CYS cc_start: 0.9273 (m) cc_final: 0.8834 (m) outliers start: 44 outliers final: 24 residues processed: 188 average time/residue: 0.5602 time to fit residues: 115.8864 Evaluate side-chains 179 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 83 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 144 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 GLN D 290 GLN C 290 GLN B 335 HIS E 95 GLN E 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.077369 restraints weight = 26611.593| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.85 r_work: 0.2913 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14718 Z= 0.123 Angle : 0.636 14.983 20077 Z= 0.302 Chirality : 0.044 0.328 2319 Planarity : 0.004 0.042 2433 Dihedral : 6.522 53.589 2972 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.22 % Allowed : 17.85 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1678 helix: 2.06 (0.21), residues: 578 sheet: 0.82 (0.27), residues: 402 loop : -0.19 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 83 TYR 0.022 0.001 TYR D 325 PHE 0.016 0.001 PHE B 319 TRP 0.036 0.001 TRP B 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00279 (14710) covalent geometry : angle 0.60505 (20055) SS BOND : bond 0.00097 ( 2) SS BOND : angle 1.05298 ( 4) hydrogen bonds : bond 0.04012 ( 670) hydrogen bonds : angle 3.84822 ( 2247) link_NAG-ASN : bond 0.01242 ( 6) link_NAG-ASN : angle 6.52436 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9013 (ttt90) cc_final: 0.8649 (ttt-90) REVERT: D 438 SER cc_start: 0.8671 (m) cc_final: 0.8458 (p) REVERT: B 83 ARG cc_start: 0.8877 (ttp-110) cc_final: 0.8608 (ttm110) REVERT: B 134 GLU cc_start: 0.7968 (pm20) cc_final: 0.7607 (tp30) REVERT: B 408 LYS cc_start: 0.8353 (ttpt) cc_final: 0.8093 (pttm) REVERT: E 136 CYS cc_start: 0.9278 (m) cc_final: 0.8859 (m) REVERT: E 284 TRP cc_start: 0.8506 (m-10) cc_final: 0.8098 (m-10) outliers start: 34 outliers final: 23 residues processed: 186 average time/residue: 0.5548 time to fit residues: 113.6050 Evaluate side-chains 179 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 4 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 149 optimal weight: 0.5980 chunk 163 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 GLN C 201 GLN C 290 GLN B 168 ASN B 335 HIS E 95 GLN E 157 GLN E 290 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.078311 restraints weight = 26466.407| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.81 r_work: 0.2932 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14718 Z= 0.119 Angle : 0.642 14.545 20077 Z= 0.301 Chirality : 0.044 0.325 2319 Planarity : 0.004 0.044 2433 Dihedral : 6.418 58.243 2972 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.09 % Allowed : 18.18 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.21), residues: 1678 helix: 2.16 (0.21), residues: 575 sheet: 0.89 (0.27), residues: 402 loop : -0.20 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 117 TYR 0.022 0.001 TYR D 325 PHE 0.014 0.001 PHE B 319 TRP 0.037 0.001 TRP B 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00272 (14710) covalent geometry : angle 0.61312 (20055) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.99526 ( 4) hydrogen bonds : bond 0.03821 ( 670) hydrogen bonds : angle 3.78322 ( 2247) link_NAG-ASN : bond 0.01193 ( 6) link_NAG-ASN : angle 6.34600 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3356 Ramachandran restraints generated. 1678 Oldfield, 0 Emsley, 1678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 83 ARG cc_start: 0.9038 (ttt90) cc_final: 0.8685 (ttt-90) REVERT: A 333 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.7259 (ttm170) REVERT: D 438 SER cc_start: 0.8640 (m) cc_final: 0.8418 (p) REVERT: C 113 MET cc_start: 0.9009 (mtp) cc_final: 0.8796 (ttt) REVERT: B 83 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8634 (ttm110) REVERT: B 134 GLU cc_start: 0.7936 (pm20) cc_final: 0.7597 (tp30) REVERT: B 408 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8099 (pttm) REVERT: E 136 CYS cc_start: 0.9288 (m) cc_final: 0.8851 (m) REVERT: E 284 TRP cc_start: 0.8469 (m-10) cc_final: 0.8072 (m-10) REVERT: E 473 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.7269 (t80) outliers start: 32 outliers final: 23 residues processed: 186 average time/residue: 0.5028 time to fit residues: 103.4566 Evaluate side-chains 183 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 473 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 GLN C 201 GLN C 290 GLN B 335 HIS E 95 GLN E 157 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.078097 restraints weight = 26557.257| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 2.82 r_work: 0.2936 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14718 Z= 0.125 Angle : 0.638 14.348 20077 Z= 0.302 Chirality : 0.045 0.329 2319 Planarity : 0.004 0.042 2433 Dihedral : 6.307 54.276 2972 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.22 % Allowed : 18.38 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.21), residues: 1678 helix: 2.15 (0.21), residues: 574 sheet: 0.92 (0.27), residues: 402 loop : -0.20 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 117 TYR 0.022 0.001 TYR D 325 PHE 0.019 0.001 PHE D 428 TRP 0.042 0.001 TRP B 263 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00290 (14710) covalent geometry : angle 0.60930 (20055) SS BOND : bond 0.00101 ( 2) SS BOND : angle 1.02514 ( 4) hydrogen bonds : bond 0.03819 ( 670) hydrogen bonds : angle 3.77591 ( 2247) link_NAG-ASN : bond 0.01175 ( 6) link_NAG-ASN : angle 6.30290 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3667.94 seconds wall clock time: 63 minutes 31.42 seconds (3811.42 seconds total)