Starting phenix.real_space_refine on Sat Aug 23 04:54:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utf_42539/08_2025/8utf_42539.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.075 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 54 5.16 5 C 6111 2.51 5 N 1647 2.21 5 O 2015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9827 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "a" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "b" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "c" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "a" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "c" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 2.06, per 1000 atoms: 0.21 Number of scatterers: 9827 At special positions: 0 Unit cell: (84.15, 86.13, 184.14, 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 54 16.00 O 2015 8.00 N 1647 7.00 C 6111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS a 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS b 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS c 195 " distance=2.03 Simple disulfide: pdb=" SG CYS a 334 " - pdb=" SG CYS a 343 " distance=2.03 Simple disulfide: pdb=" SG CYS a 358 " - pdb=" SG CYS a 366 " distance=2.03 Simple disulfide: pdb=" SG CYS a 390 " - pdb=" SG CYS a 395 " distance=2.03 Simple disulfide: pdb=" SG CYS a 397 " - pdb=" SG CYS a 420 " distance=2.03 Simple disulfide: pdb=" SG CYS b 334 " - pdb=" SG CYS b 343 " distance=2.03 Simple disulfide: pdb=" SG CYS b 358 " - pdb=" SG CYS b 366 " distance=2.03 Simple disulfide: pdb=" SG CYS b 390 " - pdb=" SG CYS b 395 " distance=2.03 Simple disulfide: pdb=" SG CYS b 397 " - pdb=" SG CYS b 420 " distance=2.03 Simple disulfide: pdb=" SG CYS c 334 " - pdb=" SG CYS c 343 " distance=2.03 Simple disulfide: pdb=" SG CYS c 358 " - pdb=" SG CYS c 366 " distance=2.03 Simple disulfide: pdb=" SG CYS c 390 " - pdb=" SG CYS c 395 " distance=2.03 Simple disulfide: pdb=" SG CYS c 397 " - pdb=" SG CYS c 420 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 61 " " NAG A 602 " - " ASN A 67 " " NAG A 603 " - " ASN A 29 " " NAG B 601 " - " ASN B 61 " " NAG B 602 " - " ASN B 67 " " NAG B 603 " - " ASN B 29 " " NAG C 601 " - " ASN C 61 " " NAG C 602 " - " ASN C 67 " " NAG C 603 " - " ASN C 29 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 344.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 44.7% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.793A pdb=" N LYS A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 Proline residue: A 86 - end of helix Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.778A pdb=" N LYS B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 95 Proline residue: B 86 - end of helix Processing helix chain 'C' and resid 30 through 33 removed outlier: 3.651A pdb=" N ILE C 33 " --> pdb=" O LEU C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 69 through 95 Proline residue: C 86 - end of helix Processing helix chain 'a' and resid 142 through 185 removed outlier: 3.605A pdb=" N THR a 156 " --> pdb=" O ALA a 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE a 164 " --> pdb=" O ALA a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 223 removed outlier: 3.565A pdb=" N TYR a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) Proline residue: a 219 - end of helix Processing helix chain 'a' and resid 230 through 238 Processing helix chain 'a' and resid 241 through 250 Processing helix chain 'a' and resid 253 through 263 removed outlier: 3.664A pdb=" N LEU a 257 " --> pdb=" O GLY a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 352 through 360 Processing helix chain 'a' and resid 362 through 366 Processing helix chain 'a' and resid 459 through 484 removed outlier: 4.823A pdb=" N ALA a 473 " --> pdb=" O LYS a 469 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS a 474 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU a 475 " --> pdb=" O GLU a 471 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU a 476 " --> pdb=" O ASP a 472 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER a 480 " --> pdb=" O LEU a 476 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP a 481 " --> pdb=" O LEU a 477 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN a 482 " --> pdb=" O GLU a 478 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 186 Processing helix chain 'b' and resid 186 through 223 Proline residue: b 219 - end of helix Processing helix chain 'b' and resid 230 through 238 Processing helix chain 'b' and resid 241 through 250 Processing helix chain 'b' and resid 253 through 263 Processing helix chain 'b' and resid 352 through 360 Processing helix chain 'b' and resid 362 through 366 Processing helix chain 'b' and resid 459 through 484 removed outlier: 3.686A pdb=" N LEU b 463 " --> pdb=" O VAL b 459 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU b 478 " --> pdb=" O LYS b 474 " (cutoff:3.500A) Processing helix chain 'c' and resid 142 through 186 removed outlier: 3.544A pdb=" N THR c 157 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 223 Proline residue: c 219 - end of helix Processing helix chain 'c' and resid 230 through 238 Processing helix chain 'c' and resid 241 through 250 Processing helix chain 'c' and resid 253 through 263 removed outlier: 3.618A pdb=" N LEU c 257 " --> pdb=" O GLY c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 361 Processing helix chain 'c' and resid 362 through 366 Processing helix chain 'c' and resid 459 through 484 removed outlier: 3.590A pdb=" N LEU c 463 " --> pdb=" O VAL c 459 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE c 483 " --> pdb=" O SER c 479 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU c 484 " --> pdb=" O SER c 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 57 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 35 through 57 current: chain 'a' and resid 266 through 273 removed outlier: 3.776A pdb=" N LYS a 266 " --> pdb=" O ALA a 284 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL a 280 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL a 272 " --> pdb=" O PHE a 278 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE a 278 " --> pdb=" O VAL a 272 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR a 318 " --> pdb=" O PHE a 329 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE a 329 " --> pdb=" O TYR a 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 325 through 329 current: chain 'a' and resid 340 through 343 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.158A pdb=" N ASN A 61 " --> pdb=" O ILE c 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 35 through 37 current: chain 'a' and resid 440 through 442 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 440 through 442 current: chain 'b' and resid 266 through 273 removed outlier: 3.783A pdb=" N LYS b 266 " --> pdb=" O ALA b 284 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL b 280 " --> pdb=" O THR b 270 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL b 272 " --> pdb=" O PHE b 278 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE b 278 " --> pdb=" O VAL b 272 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR b 318 " --> pdb=" O PHE b 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 329 " --> pdb=" O TYR b 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 325 through 329 current: chain 'b' and resid 341 through 343 Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.053A pdb=" N ASN B 61 " --> pdb=" O ILE a 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 57 removed outlier: 8.912A pdb=" N ALA b 440 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 53 " --> pdb=" O ALA b 440 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR b 442 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 55 " --> pdb=" O TYR b 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 440 through 442 current: chain 'c' and resid 266 through 273 removed outlier: 6.131A pdb=" N ALA c 267 " --> pdb=" O ALA c 284 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA c 284 " --> pdb=" O ALA c 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE c 269 " --> pdb=" O SER c 282 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER c 282 " --> pdb=" O ILE c 269 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS c 271 " --> pdb=" O VAL c 280 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR c 318 " --> pdb=" O PHE c 329 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE c 329 " --> pdb=" O TYR c 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 325 through 329 current: chain 'c' and resid 340 through 343 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.745A pdb=" N ASN C 61 " --> pdb=" O ILE b 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'a' and resid 305 through 306 Processing sheet with id=AA8, first strand: chain 'a' and resid 379 through 382 Processing sheet with id=AA9, first strand: chain 'a' and resid 403 through 404 removed outlier: 4.471A pdb=" N CYS a 395 " --> pdb=" O ILE a 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 304 through 306 Processing sheet with id=AB2, first strand: chain 'b' and resid 379 through 382 Processing sheet with id=AB3, first strand: chain 'b' and resid 395 through 397 Processing sheet with id=AB4, first strand: chain 'c' and resid 304 through 306 removed outlier: 3.959A pdb=" N GLN c 309 " --> pdb=" O ILE c 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 379 through 382 Processing sheet with id=AB6, first strand: chain 'c' and resid 403 through 404 removed outlier: 4.468A pdb=" N CYS c 395 " --> pdb=" O ILE c 404 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1410 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: 1.46 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3187 1.34 - 1.46: 1617 1.46 - 1.58: 4952 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9834 Sorted by residual: bond pdb=" CG LEU c 206 " pdb=" CD1 LEU c 206 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.20e-01 bond pdb=" CA VAL a 371 " pdb=" CB VAL a 371 " ideal model delta sigma weight residual 1.527 1.536 -0.009 1.31e-02 5.83e+03 4.99e-01 bond pdb=" CG LEU a 238 " pdb=" CD1 LEU a 238 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.88e-01 bond pdb=" CB LEU a 206 " pdb=" CG LEU a 206 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.27e-01 bond pdb=" CG LEU a 457 " pdb=" CD2 LEU a 457 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.07e-01 ... (remaining 9829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 13200 1.71 - 3.42: 115 3.42 - 5.13: 22 5.13 - 6.84: 0 6.84 - 8.55: 1 Bond angle restraints: 13338 Sorted by residual: angle pdb=" CA LEU a 206 " pdb=" CB LEU a 206 " pdb=" CG LEU a 206 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CA GLN b 383 " pdb=" CB GLN b 383 " pdb=" CG GLN b 383 " ideal model delta sigma weight residual 114.10 117.38 -3.28 2.00e+00 2.50e-01 2.68e+00 angle pdb=" OG1 THR C 47 " pdb=" CB THR C 47 " pdb=" CG2 THR C 47 " ideal model delta sigma weight residual 109.30 106.04 3.26 2.00e+00 2.50e-01 2.66e+00 angle pdb=" C SER b 382 " pdb=" N GLN b 383 " pdb=" CA GLN b 383 " ideal model delta sigma weight residual 122.82 125.02 -2.20 1.42e+00 4.96e-01 2.40e+00 angle pdb=" CA TYR b 349 " pdb=" CB TYR b 349 " pdb=" CG TYR b 349 " ideal model delta sigma weight residual 113.90 116.62 -2.72 1.80e+00 3.09e-01 2.29e+00 ... (remaining 13333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 5731 22.30 - 44.59: 296 44.59 - 66.89: 78 66.89 - 89.19: 16 89.19 - 111.49: 20 Dihedral angle restraints: 6141 sinusoidal: 2547 harmonic: 3594 Sorted by residual: dihedral pdb=" CB CYS b 397 " pdb=" SG CYS b 397 " pdb=" SG CYS b 420 " pdb=" CB CYS b 420 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS a 397 " pdb=" SG CYS a 397 " pdb=" SG CYS a 420 " pdb=" CB CYS a 420 " ideal model delta sinusoidal sigma weight residual -86.00 -129.14 43.14 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS B 68 " pdb=" SG CYS B 68 " pdb=" SG CYS b 195 " pdb=" CB CYS b 195 " ideal model delta sinusoidal sigma weight residual -86.00 -125.90 39.90 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 6138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1227 0.041 - 0.081: 240 0.081 - 0.122: 132 0.122 - 0.163: 16 0.163 - 0.203: 2 Chirality restraints: 1617 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL c 459 " pdb=" CA VAL c 459 " pdb=" CG1 VAL c 459 " pdb=" CG2 VAL c 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CB VAL a 459 " pdb=" CA VAL a 459 " pdb=" CG1 VAL a 459 " pdb=" CG2 VAL a 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 1614 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR b 349 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO b 350 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO b 350 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO b 350 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET c 337 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO c 338 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO c 338 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO c 338 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL c 315 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO c 316 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO c 316 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO c 316 " -0.015 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1386 2.76 - 3.29: 9254 3.29 - 3.83: 16096 3.83 - 4.36: 19964 4.36 - 4.90: 34264 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" OH TYR b 442 " pdb=" OE2 GLU c 212 " model vdw 2.222 3.040 nonbonded pdb=" O VAL b 302 " pdb=" O HOH b 601 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN b 346 " pdb=" O HOH b 602 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU a 212 " pdb=" OH TYR c 442 " model vdw 2.260 3.040 nonbonded pdb=" O ILE a 411 " pdb=" O HOH a 601 " model vdw 2.262 3.040 ... (remaining 80959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 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: 0.020 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.950 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:9.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9858 Z= 0.117 Angle : 0.458 8.548 13395 Z= 0.229 Chirality : 0.043 0.203 1617 Planarity : 0.004 0.031 1689 Dihedral : 16.145 111.487 3798 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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 aren not related in a simple way. whole: 0.28 (0.23), residues: 1236 helix: 0.92 (0.22), residues: 513 sheet: 1.55 (0.47), residues: 111 loop : -0.69 (0.24), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG a 263 TYR 0.016 0.001 TYR a 349 PHE 0.012 0.002 PHE a 278 TRP 0.007 0.001 TRP a 311 HIS 0.003 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9834) covalent geometry : angle 0.45489 (13338) SS BOND : bond 0.00181 ( 15) SS BOND : angle 0.51341 ( 30) hydrogen bonds : bond 0.23596 ( 493) hydrogen bonds : angle 7.49563 ( 1410) link_NAG-ASN : bond 0.00237 ( 9) link_NAG-ASN : angle 1.15179 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 66 ASN cc_start: 0.6752 (p0) cc_final: 0.6538 (p0) REVERT: A 70 ARG cc_start: 0.7340 (mmt180) cc_final: 0.6910 (mtp-110) REVERT: A 78 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7454 (ttp-110) REVERT: A 81 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7190 (mtt90) REVERT: A 85 GLU cc_start: 0.8341 (tp30) cc_final: 0.7838 (tp30) REVERT: B 85 GLU cc_start: 0.8390 (tp30) cc_final: 0.8017 (tp30) REVERT: C 85 GLU cc_start: 0.8715 (tp30) cc_final: 0.8138 (tp30) REVERT: a 185 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7626 (mm-30) REVERT: a 268 ARG cc_start: 0.7870 (ttm-80) cc_final: 0.7496 (ptm160) REVERT: a 275 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8256 (mp0) REVERT: a 292 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7311 (ptmm) REVERT: a 317 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8441 (mtmt) REVERT: a 337 MET cc_start: 0.8227 (mtm) cc_final: 0.7833 (mtm) REVERT: a 357 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7534 (mt-10) REVERT: a 364 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7265 (mppt) REVERT: a 445 ARG cc_start: 0.8010 (ttm110) cc_final: 0.7678 (mtp85) REVERT: b 205 LYS cc_start: 0.8498 (mttm) cc_final: 0.8235 (mttp) REVERT: b 226 SER cc_start: 0.8834 (t) cc_final: 0.8488 (p) REVERT: b 266 LYS cc_start: 0.8712 (mmtp) cc_final: 0.8181 (mmtt) REVERT: b 364 LYS cc_start: 0.8055 (mttt) cc_final: 0.7579 (mppt) REVERT: b 396 LYS cc_start: 0.8175 (ptmt) cc_final: 0.7890 (ptmm) REVERT: b 399 THR cc_start: 0.8395 (m) cc_final: 0.8167 (p) REVERT: b 445 ARG cc_start: 0.8437 (ttm110) cc_final: 0.7800 (ttt90) REVERT: c 247 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7185 (tt0) REVERT: c 292 LYS cc_start: 0.8216 (pttp) cc_final: 0.7443 (mmtm) REVERT: c 357 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6121 (mt-10) REVERT: c 364 LYS cc_start: 0.7832 (mppt) cc_final: 0.7536 (mppt) REVERT: c 372 SER cc_start: 0.8847 (t) cc_final: 0.8548 (p) REVERT: c 410 LYS cc_start: 0.7095 (mmtm) cc_final: 0.6127 (ptpp) REVERT: c 435 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7246 (ttt180) REVERT: c 445 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7949 (ttm110) outliers start: 0 outliers final: 2 residues processed: 215 average time/residue: 0.5488 time to fit residues: 125.1821 Evaluate side-chains 152 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain a residue 447 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN a 158 ASN a 297 HIS a 389 ASN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.149482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101439 restraints weight = 10530.972| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.77 r_work: 0.2951 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 9858 Z= 0.197 Angle : 0.643 12.735 13395 Z= 0.322 Chirality : 0.049 0.356 1617 Planarity : 0.005 0.035 1689 Dihedral : 11.130 97.148 1549 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.59 % Allowed : 8.40 % Favored : 90.01 % 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 aren not related in a simple way. whole: 0.98 (0.23), residues: 1236 helix: 1.96 (0.21), residues: 528 sheet: 1.70 (0.46), residues: 114 loop : -0.81 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 70 TYR 0.021 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.006 0.001 TRP a 311 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9834) covalent geometry : angle 0.62252 (13338) SS BOND : bond 0.00152 ( 15) SS BOND : angle 2.62108 ( 30) hydrogen bonds : bond 0.05924 ( 493) hydrogen bonds : angle 4.66195 ( 1410) link_NAG-ASN : bond 0.01314 ( 9) link_NAG-ASN : angle 2.48430 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.234 Fit side-chains REVERT: A 78 ARG cc_start: 0.8709 (ttp80) cc_final: 0.8221 (ttm-80) REVERT: A 81 ARG cc_start: 0.8117 (mtt-85) cc_final: 0.7806 (mtm110) REVERT: B 46 MET cc_start: 0.9196 (mtm) cc_final: 0.8933 (mtp) REVERT: B 85 GLU cc_start: 0.8522 (tp30) cc_final: 0.8288 (tp30) REVERT: C 75 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 85 GLU cc_start: 0.8684 (tp30) cc_final: 0.8270 (tp30) REVERT: a 171 MET cc_start: 0.8050 (mtm) cc_final: 0.7845 (mtp) REVERT: a 292 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7694 (ptmm) REVERT: a 337 MET cc_start: 0.8547 (mtm) cc_final: 0.8082 (mtt) REVERT: a 364 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7725 (mppt) REVERT: a 424 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7621 (tt0) REVERT: b 266 LYS cc_start: 0.8853 (mmtp) cc_final: 0.8461 (mmtt) REVERT: b 364 LYS cc_start: 0.8170 (mttt) cc_final: 0.7921 (mppt) REVERT: b 411 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7964 (mm) REVERT: b 445 ARG cc_start: 0.8616 (ttm110) cc_final: 0.8193 (mtp180) REVERT: c 292 LYS cc_start: 0.8365 (pttp) cc_final: 0.7962 (mmtm) REVERT: c 410 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6738 (ptpp) REVERT: c 435 ARG cc_start: 0.8065 (ttt90) cc_final: 0.7793 (ttt180) outliers start: 17 outliers final: 6 residues processed: 148 average time/residue: 0.5936 time to fit residues: 92.9660 Evaluate side-chains 136 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 141 MET Chi-restraints excluded: chain a residue 247 GLU Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain c residue 400 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN C 24 GLN b 183 ASN b 200 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100195 restraints weight = 10616.223| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.79 r_work: 0.2932 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9858 Z= 0.196 Angle : 0.613 7.550 13395 Z= 0.306 Chirality : 0.047 0.265 1617 Planarity : 0.005 0.049 1689 Dihedral : 7.727 59.361 1545 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.43 % Allowed : 10.83 % Favored : 86.74 % 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 aren not related in a simple way. whole: 1.13 (0.23), residues: 1236 helix: 2.27 (0.22), residues: 531 sheet: 1.54 (0.48), residues: 111 loop : -0.88 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 445 TYR 0.020 0.002 TYR b 210 PHE 0.015 0.002 PHE c 278 TRP 0.007 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 9834) covalent geometry : angle 0.59766 (13338) SS BOND : bond 0.00317 ( 15) SS BOND : angle 1.48725 ( 30) hydrogen bonds : bond 0.05195 ( 493) hydrogen bonds : angle 4.31605 ( 1410) link_NAG-ASN : bond 0.01003 ( 9) link_NAG-ASN : angle 2.71540 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8183 (ttm-80) REVERT: A 81 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7787 (mtm110) REVERT: B 46 MET cc_start: 0.9204 (mtm) cc_final: 0.8955 (mtp) REVERT: B 85 GLU cc_start: 0.8505 (tp30) cc_final: 0.8195 (tp30) REVERT: C 57 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8417 (mmtt) REVERT: C 75 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8031 (mm-30) REVERT: C 85 GLU cc_start: 0.8526 (tp30) cc_final: 0.8311 (tp30) REVERT: a 292 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7697 (ptmm) REVERT: a 337 MET cc_start: 0.8515 (mtm) cc_final: 0.7976 (mtt) REVERT: a 364 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7733 (mppt) REVERT: a 424 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7586 (tt0) REVERT: b 266 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8472 (mmtt) REVERT: b 275 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: b 364 LYS cc_start: 0.8107 (mttt) cc_final: 0.7882 (mppt) REVERT: b 411 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7942 (mm) REVERT: b 445 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8204 (mtp180) REVERT: c 292 LYS cc_start: 0.8320 (pttp) cc_final: 0.7970 (mmtm) REVERT: c 410 LYS cc_start: 0.7572 (mmtm) cc_final: 0.6714 (ptpp) REVERT: c 435 ARG cc_start: 0.7984 (ttt90) cc_final: 0.7734 (ttt180) outliers start: 26 outliers final: 8 residues processed: 144 average time/residue: 0.5881 time to fit residues: 90.0209 Evaluate side-chains 130 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain a residue 247 GLU Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 275 GLU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain c residue 400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN a 158 ASN c 406 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.149380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101243 restraints weight = 10635.402| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.77 r_work: 0.2960 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9858 Z= 0.173 Angle : 0.572 7.175 13395 Z= 0.290 Chirality : 0.046 0.325 1617 Planarity : 0.004 0.046 1689 Dihedral : 6.139 52.150 1545 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.33 % Allowed : 11.95 % Favored : 85.71 % 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 aren not related in a simple way. whole: 1.24 (0.24), residues: 1236 helix: 2.48 (0.22), residues: 531 sheet: 1.48 (0.48), residues: 111 loop : -0.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 445 TYR 0.019 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9834) covalent geometry : angle 0.55744 (13338) SS BOND : bond 0.00459 ( 15) SS BOND : angle 1.62945 ( 30) hydrogen bonds : bond 0.04607 ( 493) hydrogen bonds : angle 4.17254 ( 1410) link_NAG-ASN : bond 0.01296 ( 9) link_NAG-ASN : angle 2.42331 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8671 (ttp80) cc_final: 0.8139 (ttm-80) REVERT: A 81 ARG cc_start: 0.8088 (mtt-85) cc_final: 0.7752 (mtm110) REVERT: B 46 MET cc_start: 0.9186 (mtm) cc_final: 0.8947 (mtp) REVERT: B 85 GLU cc_start: 0.8477 (tp30) cc_final: 0.8143 (tp30) REVERT: C 75 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7984 (mm-30) REVERT: a 292 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7683 (ptmm) REVERT: a 337 MET cc_start: 0.8480 (mtm) cc_final: 0.7933 (mtt) REVERT: a 364 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7603 (mppt) REVERT: a 424 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7550 (tt0) REVERT: b 247 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7423 (tm-30) REVERT: b 266 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8435 (mmtt) REVERT: b 275 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: b 364 LYS cc_start: 0.8116 (mttt) cc_final: 0.7852 (mppt) REVERT: b 445 ARG cc_start: 0.8599 (ttm110) cc_final: 0.8138 (mtp180) REVERT: c 292 LYS cc_start: 0.8312 (pttp) cc_final: 0.7933 (mmtm) REVERT: c 410 LYS cc_start: 0.7541 (mmtm) cc_final: 0.6621 (ptpp) outliers start: 25 outliers final: 10 residues processed: 138 average time/residue: 0.5808 time to fit residues: 85.2443 Evaluate side-chains 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 275 GLU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 116 optimal weight: 0.0980 chunk 64 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.148665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100673 restraints weight = 10512.661| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.80 r_work: 0.2955 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9858 Z= 0.175 Angle : 0.577 9.412 13395 Z= 0.291 Chirality : 0.046 0.432 1617 Planarity : 0.004 0.038 1689 Dihedral : 5.932 54.778 1545 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.71 % Allowed : 12.04 % Favored : 85.25 % 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 aren not related in a simple way. whole: 1.30 (0.24), residues: 1236 helix: 2.58 (0.22), residues: 531 sheet: 1.45 (0.47), residues: 111 loop : -0.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 445 TYR 0.019 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9834) covalent geometry : angle 0.55200 (13338) SS BOND : bond 0.00336 ( 15) SS BOND : angle 1.73038 ( 30) hydrogen bonds : bond 0.04476 ( 493) hydrogen bonds : angle 4.12309 ( 1410) link_NAG-ASN : bond 0.00872 ( 9) link_NAG-ASN : angle 3.36042 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.321 Fit side-chains REVERT: A 78 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8049 (ttm-80) REVERT: A 81 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7691 (mtm110) REVERT: B 46 MET cc_start: 0.9190 (mtm) cc_final: 0.8951 (mtp) REVERT: B 85 GLU cc_start: 0.8425 (tp30) cc_final: 0.8044 (tp30) REVERT: B 92 ASN cc_start: 0.8732 (t0) cc_final: 0.8531 (t0) REVERT: C 57 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8301 (mmtt) REVERT: C 67 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6949 (m-40) REVERT: C 75 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7914 (mm-30) REVERT: a 292 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7630 (ptmm) REVERT: a 337 MET cc_start: 0.8491 (mtm) cc_final: 0.7997 (mtt) REVERT: a 364 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7543 (mppt) REVERT: a 424 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7485 (tt0) REVERT: b 247 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: b 266 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8414 (mmtt) REVERT: b 364 LYS cc_start: 0.8121 (mttt) cc_final: 0.7821 (mppt) REVERT: b 445 ARG cc_start: 0.8452 (ttm110) cc_final: 0.8057 (mtp180) REVERT: c 292 LYS cc_start: 0.8320 (pttp) cc_final: 0.7896 (mmtm) REVERT: c 410 LYS cc_start: 0.7514 (mmtm) cc_final: 0.6601 (ptpp) outliers start: 29 outliers final: 12 residues processed: 143 average time/residue: 0.5463 time to fit residues: 83.2488 Evaluate side-chains 143 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 128 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 67 ASN Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 14 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 96 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN a 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100101 restraints weight = 10571.150| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.81 r_work: 0.2932 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9858 Z= 0.188 Angle : 0.580 7.786 13395 Z= 0.296 Chirality : 0.046 0.204 1617 Planarity : 0.004 0.045 1689 Dihedral : 5.858 52.548 1545 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.80 % Allowed : 12.14 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.24), residues: 1236 helix: 2.59 (0.22), residues: 528 sheet: 1.42 (0.47), residues: 111 loop : -0.93 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG c 445 TYR 0.020 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 9834) covalent geometry : angle 0.56449 (13338) SS BOND : bond 0.00504 ( 15) SS BOND : angle 1.89799 ( 30) hydrogen bonds : bond 0.04465 ( 493) hydrogen bonds : angle 4.11661 ( 1410) link_NAG-ASN : bond 0.00874 ( 9) link_NAG-ASN : angle 2.29408 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.392 Fit side-chains REVERT: A 78 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8163 (ttm-80) REVERT: A 81 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7828 (mtm110) REVERT: C 75 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8016 (mm-30) REVERT: C 85 GLU cc_start: 0.8700 (tp30) cc_final: 0.8437 (tp30) REVERT: a 292 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7735 (ptmm) REVERT: a 337 MET cc_start: 0.8509 (mtm) cc_final: 0.8078 (mtt) REVERT: a 364 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7611 (mppt) REVERT: a 424 GLU cc_start: 0.8398 (mt-10) cc_final: 0.7624 (tt0) REVERT: b 171 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7459 (ttp) REVERT: b 247 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: b 266 LYS cc_start: 0.8843 (mmtp) cc_final: 0.8476 (mmtt) REVERT: b 364 LYS cc_start: 0.8124 (mttt) cc_final: 0.7872 (mppt) REVERT: b 445 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8221 (mtp180) REVERT: c 216 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8634 (mp) REVERT: c 292 LYS cc_start: 0.8326 (pttp) cc_final: 0.7943 (mmtm) REVERT: c 410 LYS cc_start: 0.7620 (mmtm) cc_final: 0.6714 (ptpp) outliers start: 30 outliers final: 14 residues processed: 147 average time/residue: 0.5841 time to fit residues: 91.4107 Evaluate side-chains 147 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 73 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.148570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.100316 restraints weight = 10580.363| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.78 r_work: 0.2947 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9858 Z= 0.214 Angle : 0.614 10.630 13395 Z= 0.311 Chirality : 0.047 0.328 1617 Planarity : 0.005 0.050 1689 Dihedral : 5.685 52.711 1545 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.43 % Allowed : 13.35 % Favored : 84.22 % 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 aren not related in a simple way. whole: 1.23 (0.24), residues: 1236 helix: 2.56 (0.22), residues: 528 sheet: 1.31 (0.47), residues: 111 loop : -0.96 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 445 TYR 0.021 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP B 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 9834) covalent geometry : angle 0.58646 (13338) SS BOND : bond 0.00409 ( 15) SS BOND : angle 2.10316 ( 30) hydrogen bonds : bond 0.04544 ( 493) hydrogen bonds : angle 4.15360 ( 1410) link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 3.46492 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.328 Fit side-chains REVERT: A 78 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8165 (ttm-80) REVERT: A 81 ARG cc_start: 0.8162 (mtt-85) cc_final: 0.7794 (mtm110) REVERT: C 75 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7984 (mm-30) REVERT: C 85 GLU cc_start: 0.8701 (tp30) cc_final: 0.8434 (tp30) REVERT: a 247 GLU cc_start: 0.7756 (tt0) cc_final: 0.7522 (tm-30) REVERT: a 292 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7751 (ptmm) REVERT: a 337 MET cc_start: 0.8594 (mtm) cc_final: 0.8022 (mtt) REVERT: a 364 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7614 (mppt) REVERT: a 424 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7592 (tt0) REVERT: b 247 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7403 (tm-30) REVERT: b 266 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8451 (mmtt) REVERT: b 364 LYS cc_start: 0.8152 (mttt) cc_final: 0.7838 (mppt) REVERT: b 445 ARG cc_start: 0.8574 (ttm110) cc_final: 0.8156 (mtp180) REVERT: c 216 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8562 (mp) REVERT: c 292 LYS cc_start: 0.8317 (pttp) cc_final: 0.7944 (mmtm) REVERT: c 410 LYS cc_start: 0.7607 (mmtm) cc_final: 0.6686 (ptpp) outliers start: 26 outliers final: 14 residues processed: 140 average time/residue: 0.6159 time to fit residues: 91.6410 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 0.0980 chunk 106 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100927 restraints weight = 10502.820| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.83 r_work: 0.2958 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9858 Z= 0.154 Angle : 0.571 11.044 13395 Z= 0.289 Chirality : 0.045 0.436 1617 Planarity : 0.004 0.054 1689 Dihedral : 5.733 52.768 1545 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 14.01 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.24), residues: 1236 helix: 2.55 (0.22), residues: 537 sheet: 1.34 (0.47), residues: 111 loop : -0.86 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG c 445 TYR 0.018 0.001 TYR c 210 PHE 0.013 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9834) covalent geometry : angle 0.53694 (13338) SS BOND : bond 0.00361 ( 15) SS BOND : angle 2.08269 ( 30) hydrogen bonds : bond 0.04116 ( 493) hydrogen bonds : angle 4.05411 ( 1410) link_NAG-ASN : bond 0.00716 ( 9) link_NAG-ASN : angle 3.83353 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.369 Fit side-chains REVERT: A 78 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8062 (ttm-80) REVERT: A 81 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7748 (mtm110) REVERT: C 75 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7898 (mm-30) REVERT: a 247 GLU cc_start: 0.7725 (tt0) cc_final: 0.7455 (tm-30) REVERT: a 292 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7689 (ptmm) REVERT: a 337 MET cc_start: 0.8541 (mtm) cc_final: 0.7956 (mtt) REVERT: a 364 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7545 (mppt) REVERT: a 424 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7388 (tm-30) REVERT: b 171 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7528 (ttp) REVERT: b 247 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: b 266 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8372 (mmtt) REVERT: b 364 LYS cc_start: 0.8128 (mttt) cc_final: 0.7793 (mppt) REVERT: b 445 ARG cc_start: 0.8417 (ttm110) cc_final: 0.8042 (mtp180) REVERT: c 216 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8445 (mp) REVERT: c 268 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7955 (ttp-170) REVERT: c 292 LYS cc_start: 0.8320 (pttp) cc_final: 0.7889 (mmtm) REVERT: c 410 LYS cc_start: 0.7542 (mmtm) cc_final: 0.6590 (ptpp) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 0.6306 time to fit residues: 94.4381 Evaluate side-chains 137 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 28 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.148121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099860 restraints weight = 10463.766| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.77 r_work: 0.2931 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9858 Z= 0.203 Angle : 0.605 8.616 13395 Z= 0.308 Chirality : 0.045 0.195 1617 Planarity : 0.005 0.059 1689 Dihedral : 5.688 52.755 1545 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.33 % Allowed : 14.38 % Favored : 83.29 % 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 aren not related in a simple way. whole: 1.26 (0.24), residues: 1236 helix: 2.52 (0.22), residues: 534 sheet: 1.26 (0.47), residues: 111 loop : -0.89 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 445 TYR 0.020 0.002 TYR b 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9834) covalent geometry : angle 0.57866 (13338) SS BOND : bond 0.00446 ( 15) SS BOND : angle 2.45527 ( 30) hydrogen bonds : bond 0.04442 ( 493) hydrogen bonds : angle 4.13672 ( 1410) link_NAG-ASN : bond 0.00505 ( 9) link_NAG-ASN : angle 3.03455 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.369 Fit side-chains REVERT: A 78 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8200 (ttm-80) REVERT: A 81 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7842 (mtm110) REVERT: C 75 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7988 (mm-30) REVERT: a 247 GLU cc_start: 0.7781 (tt0) cc_final: 0.7543 (tm-30) REVERT: a 292 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7799 (ptmm) REVERT: a 337 MET cc_start: 0.8580 (mtm) cc_final: 0.8011 (mtt) REVERT: a 364 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7629 (mppt) REVERT: a 424 GLU cc_start: 0.8397 (mt-10) cc_final: 0.7631 (tt0) REVERT: b 247 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: b 266 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8483 (mmtt) REVERT: b 364 LYS cc_start: 0.8168 (mttt) cc_final: 0.7866 (mppt) REVERT: b 445 ARG cc_start: 0.8556 (ttm110) cc_final: 0.8194 (mtp180) REVERT: c 216 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8577 (mp) REVERT: c 247 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: c 292 LYS cc_start: 0.8298 (pttp) cc_final: 0.7949 (mmtm) REVERT: c 410 LYS cc_start: 0.7654 (mmtm) cc_final: 0.6744 (ptpp) outliers start: 25 outliers final: 13 residues processed: 141 average time/residue: 0.6252 time to fit residues: 94.0391 Evaluate side-chains 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 247 GLU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.099993 restraints weight = 10423.137| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.76 r_work: 0.2933 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9858 Z= 0.210 Angle : 0.631 10.002 13395 Z= 0.319 Chirality : 0.046 0.332 1617 Planarity : 0.005 0.062 1689 Dihedral : 5.588 52.686 1545 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.96 % Allowed : 14.57 % Favored : 83.47 % 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 aren not related in a simple way. whole: 1.21 (0.24), residues: 1236 helix: 2.45 (0.22), residues: 537 sheet: 1.22 (0.47), residues: 111 loop : -0.90 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 445 TYR 0.020 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00510 ( 9834) covalent geometry : angle 0.59286 (13338) SS BOND : bond 0.00453 ( 15) SS BOND : angle 2.65515 ( 30) hydrogen bonds : bond 0.04420 ( 493) hydrogen bonds : angle 4.15290 ( 1410) link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 4.01285 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.285 Fit side-chains REVERT: A 78 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8180 (ttm-80) REVERT: A 81 ARG cc_start: 0.8104 (mtt-85) cc_final: 0.7808 (mtm110) REVERT: C 75 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7979 (mm-30) REVERT: a 190 MET cc_start: 0.8279 (tpp) cc_final: 0.8016 (tpp) REVERT: a 247 GLU cc_start: 0.7763 (tt0) cc_final: 0.7533 (tm-30) REVERT: a 292 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7802 (ptmm) REVERT: a 337 MET cc_start: 0.8582 (mtm) cc_final: 0.7997 (mtt) REVERT: a 364 LYS cc_start: 0.7994 (mmmt) cc_final: 0.7591 (mppt) REVERT: a 424 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7628 (tt0) REVERT: b 247 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: b 266 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8486 (mmtt) REVERT: b 364 LYS cc_start: 0.8191 (mttt) cc_final: 0.7873 (mppt) REVERT: b 445 ARG cc_start: 0.8550 (ttm110) cc_final: 0.8173 (mtp180) REVERT: c 216 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8567 (mp) REVERT: c 247 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: c 292 LYS cc_start: 0.8308 (pttp) cc_final: 0.7976 (mmtm) REVERT: c 410 LYS cc_start: 0.7663 (mmtm) cc_final: 0.6754 (ptpp) outliers start: 21 outliers final: 16 residues processed: 138 average time/residue: 0.6088 time to fit residues: 89.2498 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 195 CYS Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 247 GLU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 457 LEU Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.100129 restraints weight = 10504.689| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.77 r_work: 0.2934 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9858 Z= 0.197 Angle : 0.622 11.317 13395 Z= 0.315 Chirality : 0.047 0.496 1617 Planarity : 0.004 0.062 1689 Dihedral : 5.580 52.687 1545 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.05 % Allowed : 14.57 % Favored : 83.38 % 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 aren not related in a simple way. whole: 1.24 (0.24), residues: 1236 helix: 2.52 (0.22), residues: 534 sheet: 1.23 (0.47), residues: 111 loop : -0.92 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG c 445 TYR 0.020 0.002 TYR c 210 PHE 0.014 0.002 PHE c 278 TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 9834) covalent geometry : angle 0.57900 (13338) SS BOND : bond 0.00487 ( 15) SS BOND : angle 2.69973 ( 30) hydrogen bonds : bond 0.04337 ( 493) hydrogen bonds : angle 4.13771 ( 1410) link_NAG-ASN : bond 0.00597 ( 9) link_NAG-ASN : angle 4.25666 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3729.99 seconds wall clock time: 64 minutes 10.16 seconds (3850.16 seconds total)