Starting phenix.real_space_refine on Tue May 13 07:10:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utf_42539/05_2025/8utf_42539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utf_42539/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8utf_42539/05_2025/8utf_42539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utf_42539/05_2025/8utf_42539.map" model { file = "/net/cci-nas-00/data/ceres_data/8utf_42539/05_2025/8utf_42539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utf_42539/05_2025/8utf_42539.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.075 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.31, per 1000 atoms: 0.74 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.08 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: 3.55 Time building geometry restraints manager: 2.72 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: 0.03 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: 6.250 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 28.280 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.170 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (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 TRP 0.007 0.001 TRP a 311 HIS 0.003 0.001 HIS a 444 PHE 0.012 0.002 PHE a 278 TYR 0.016 0.001 TYR a 349 ARG 0.003 0.001 ARG a 263 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 9) link_NAG-ASN : angle 1.15179 ( 27) hydrogen bonds : bond 0.23596 ( 493) hydrogen bonds : angle 7.49563 ( 1410) SS BOND : bond 0.00181 ( 15) SS BOND : angle 0.51341 ( 30) covalent geometry : bond 0.00278 ( 9834) covalent geometry : angle 0.45489 (13338) *********************** 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 : 1.336 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: 1.4146 time to fit residues: 323.4567 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 : 0.998 ------------------------------------------------------------------------------- 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 103 optimal weight: 0.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.100937 restraints weight = 10486.849| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.74 r_work: 0.2938 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 9858 Z= 0.229 Angle : 0.669 13.491 13395 Z= 0.336 Chirality : 0.049 0.341 1617 Planarity : 0.005 0.038 1689 Dihedral : 11.457 99.339 1549 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.59 % Allowed : 8.96 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.23), residues: 1236 helix: 1.89 (0.21), residues: 528 sheet: 1.63 (0.46), residues: 114 loop : -0.85 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 311 HIS 0.006 0.001 HIS a 444 PHE 0.015 0.002 PHE c 278 TYR 0.022 0.002 TYR c 210 ARG 0.006 0.001 ARG b 222 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 9) link_NAG-ASN : angle 2.37267 ( 27) hydrogen bonds : bond 0.06165 ( 493) hydrogen bonds : angle 4.71769 ( 1410) SS BOND : bond 0.00425 ( 15) SS BOND : angle 2.86766 ( 30) covalent geometry : bond 0.00548 ( 9834) covalent geometry : angle 0.64765 (13338) *********************** 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 156 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.157 Fit side-chains REVERT: A 78 ARG cc_start: 0.8684 (ttp80) cc_final: 0.8187 (ttm-80) REVERT: A 81 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7804 (mtm110) REVERT: B 46 MET cc_start: 0.9202 (mtm) cc_final: 0.8946 (mtp) REVERT: B 85 GLU cc_start: 0.8555 (tp30) cc_final: 0.8308 (tp30) REVERT: C 75 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8004 (mm-30) REVERT: C 85 GLU cc_start: 0.8699 (tp30) cc_final: 0.8285 (tp30) REVERT: a 171 MET cc_start: 0.8035 (mtm) cc_final: 0.7830 (mtp) REVERT: a 292 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7762 (ptmm) REVERT: a 337 MET cc_start: 0.8541 (mtm) cc_final: 0.8037 (mtt) REVERT: a 364 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7729 (mppt) REVERT: a 424 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7619 (tt0) REVERT: b 266 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8467 (mmtt) REVERT: b 364 LYS cc_start: 0.8155 (mttt) cc_final: 0.7917 (mppt) REVERT: b 411 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7957 (mm) REVERT: b 445 ARG cc_start: 0.8621 (ttm110) cc_final: 0.8203 (mtp180) REVERT: c 292 LYS cc_start: 0.8315 (pttp) cc_final: 0.7975 (mmtm) REVERT: c 410 LYS cc_start: 0.7651 (mmtm) cc_final: 0.6752 (ptpp) REVERT: c 435 ARG cc_start: 0.7966 (ttt90) cc_final: 0.7741 (ttt180) outliers start: 17 outliers final: 6 residues processed: 143 average time/residue: 1.4114 time to fit residues: 214.5405 Evaluate side-chains 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 34 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.148064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.100474 restraints weight = 10667.535| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.77 r_work: 0.2934 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9858 Z= 0.191 Angle : 0.604 7.741 13395 Z= 0.303 Chirality : 0.047 0.261 1617 Planarity : 0.005 0.053 1689 Dihedral : 7.698 59.830 1545 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 10.74 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.23), residues: 1236 helix: 2.27 (0.22), residues: 531 sheet: 1.47 (0.48), residues: 111 loop : -0.91 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 PHE 0.015 0.002 PHE c 278 TYR 0.020 0.002 TYR c 210 ARG 0.009 0.001 ARG a 445 Details of bonding type rmsd link_NAG-ASN : bond 0.01093 ( 9) link_NAG-ASN : angle 2.50419 ( 27) hydrogen bonds : bond 0.05102 ( 493) hydrogen bonds : angle 4.28742 ( 1410) SS BOND : bond 0.00436 ( 15) SS BOND : angle 1.38176 ( 30) covalent geometry : bond 0.00449 ( 9834) covalent geometry : angle 0.59103 (13338) *********************** 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 155 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8186 (ttm-80) REVERT: A 81 ARG cc_start: 0.8091 (mtt-85) cc_final: 0.7777 (mtm110) REVERT: B 46 MET cc_start: 0.9199 (mtm) cc_final: 0.8958 (mtp) REVERT: B 85 GLU cc_start: 0.8504 (tp30) cc_final: 0.8192 (tp30) REVERT: C 57 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8384 (mmtt) REVERT: C 75 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8040 (mm-30) REVERT: C 85 GLU cc_start: 0.8582 (tp30) cc_final: 0.8333 (tp30) REVERT: a 292 LYS cc_start: 0.8056 (mmtt) cc_final: 0.7705 (ptmm) REVERT: a 337 MET cc_start: 0.8516 (mtm) cc_final: 0.8035 (mtt) REVERT: a 364 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7656 (mppt) REVERT: a 424 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7596 (tt0) REVERT: b 247 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: b 266 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8473 (mmtt) REVERT: b 275 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: b 364 LYS cc_start: 0.8130 (mttt) cc_final: 0.7894 (mppt) REVERT: b 445 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8201 (mtp180) REVERT: c 292 LYS cc_start: 0.8323 (pttp) cc_final: 0.7952 (mmtm) REVERT: c 410 LYS cc_start: 0.7586 (mmtm) cc_final: 0.6738 (ptpp) REVERT: c 435 ARG cc_start: 0.7983 (ttt90) cc_final: 0.7724 (ttt180) outliers start: 23 outliers final: 8 residues processed: 141 average time/residue: 1.4408 time to fit residues: 215.6007 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 b 183 ASN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101045 restraints weight = 10453.106| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.74 r_work: 0.2954 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9858 Z= 0.182 Angle : 0.582 8.994 13395 Z= 0.294 Chirality : 0.047 0.409 1617 Planarity : 0.004 0.048 1689 Dihedral : 6.187 52.137 1545 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 11.67 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.23), residues: 1236 helix: 2.46 (0.22), residues: 531 sheet: 1.42 (0.47), residues: 111 loop : -0.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.020 0.002 TYR c 210 ARG 0.007 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.01214 ( 9) link_NAG-ASN : angle 2.88161 ( 27) hydrogen bonds : bond 0.04665 ( 493) hydrogen bonds : angle 4.17862 ( 1410) SS BOND : bond 0.00274 ( 15) SS BOND : angle 1.64192 ( 30) covalent geometry : bond 0.00430 ( 9834) covalent geometry : angle 0.56314 (13338) *********************** 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 152 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8189 (ttm-80) REVERT: A 81 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7816 (mtm110) REVERT: B 46 MET cc_start: 0.9202 (mtm) cc_final: 0.8962 (mtp) REVERT: B 85 GLU cc_start: 0.8428 (tp30) cc_final: 0.8104 (tp30) REVERT: C 75 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8033 (mm-30) REVERT: C 85 GLU cc_start: 0.8611 (tp30) cc_final: 0.8272 (tp30) REVERT: a 292 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7722 (ptmm) REVERT: a 337 MET cc_start: 0.8514 (mtm) cc_final: 0.8013 (mtt) REVERT: a 364 LYS cc_start: 0.8041 (mmmt) cc_final: 0.7627 (mppt) REVERT: a 424 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7612 (tt0) REVERT: b 247 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7464 (tm-30) REVERT: b 266 LYS cc_start: 0.8829 (mmtp) cc_final: 0.8453 (mmtt) REVERT: b 364 LYS cc_start: 0.8171 (mttt) cc_final: 0.7884 (mppt) REVERT: b 445 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8134 (mtp180) REVERT: c 292 LYS cc_start: 0.8317 (pttp) cc_final: 0.7967 (mmtm) REVERT: c 410 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6677 (ptpp) outliers start: 25 outliers final: 10 residues processed: 138 average time/residue: 1.3961 time to fit residues: 204.9892 Evaluate side-chains 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR 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 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 77 optimal weight: 1.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN a 406 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.101295 restraints weight = 10521.112| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.80 r_work: 0.2949 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9858 Z= 0.147 Angle : 0.546 7.597 13395 Z= 0.278 Chirality : 0.045 0.285 1617 Planarity : 0.004 0.040 1689 Dihedral : 5.661 52.296 1545 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.89 % Allowed : 11.58 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1236 helix: 2.60 (0.22), residues: 531 sheet: 1.48 (0.47), residues: 111 loop : -0.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.008 0.000 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00838 ( 9) link_NAG-ASN : angle 2.44250 ( 27) hydrogen bonds : bond 0.04261 ( 493) hydrogen bonds : angle 4.05266 ( 1410) SS BOND : bond 0.00348 ( 15) SS BOND : angle 1.72786 ( 30) covalent geometry : bond 0.00338 ( 9834) covalent geometry : angle 0.52933 (13338) *********************** 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 156 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.999 Fit side-chains REVERT: A 78 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8171 (ttm-80) REVERT: A 81 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7808 (mtm110) REVERT: B 46 MET cc_start: 0.9225 (mtm) cc_final: 0.8986 (mtp) REVERT: C 57 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8367 (mmtt) REVERT: C 75 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7991 (mm-30) REVERT: C 85 GLU cc_start: 0.8586 (tp30) cc_final: 0.8335 (tp30) REVERT: C 89 ASP cc_start: 0.8435 (t0) cc_final: 0.8198 (t0) REVERT: a 292 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7689 (ptmm) REVERT: a 337 MET cc_start: 0.8470 (mtm) cc_final: 0.8042 (mtt) REVERT: a 364 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7603 (mppt) REVERT: a 424 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7508 (tm-30) REVERT: a 445 ARG cc_start: 0.8359 (mtp-110) cc_final: 0.8019 (mtp180) REVERT: b 247 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: b 266 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8466 (mmtt) REVERT: b 364 LYS cc_start: 0.8117 (mttt) cc_final: 0.7888 (mppt) REVERT: b 445 ARG cc_start: 0.8628 (ttm110) cc_final: 0.8195 (mtp180) REVERT: c 268 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7966 (ttp-170) REVERT: c 292 LYS cc_start: 0.8316 (pttp) cc_final: 0.7942 (mmtm) REVERT: c 410 LYS cc_start: 0.7593 (mmtm) cc_final: 0.6703 (ptpp) outliers start: 31 outliers final: 12 residues processed: 142 average time/residue: 1.3790 time to fit residues: 208.7297 Evaluate side-chains 135 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS 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 27 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 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 66 ASN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102856 restraints weight = 10614.112| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.03 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9858 Z= 0.173 Angle : 0.577 10.447 13395 Z= 0.292 Chirality : 0.046 0.396 1617 Planarity : 0.004 0.049 1689 Dihedral : 5.693 52.558 1545 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.89 % Allowed : 12.42 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1236 helix: 2.64 (0.22), residues: 528 sheet: 1.46 (0.47), residues: 111 loop : -0.95 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.020 0.002 TYR c 210 ARG 0.010 0.000 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.01050 ( 9) link_NAG-ASN : angle 3.31876 ( 27) hydrogen bonds : bond 0.04314 ( 493) hydrogen bonds : angle 4.05059 ( 1410) SS BOND : bond 0.00357 ( 15) SS BOND : angle 1.84255 ( 30) covalent geometry : bond 0.00412 ( 9834) covalent geometry : angle 0.55135 (13338) *********************** 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 160 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.070 Fit side-chains REVERT: A 78 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8182 (ttm-80) REVERT: A 81 ARG cc_start: 0.8148 (mtt-85) cc_final: 0.7828 (mtm110) REVERT: B 46 MET cc_start: 0.9234 (mtm) cc_final: 0.9007 (mtp) REVERT: C 57 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8346 (mmtt) REVERT: C 75 GLU cc_start: 0.8273 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 85 GLU cc_start: 0.8600 (tp30) cc_final: 0.8344 (tp30) REVERT: a 292 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7695 (ptmm) REVERT: a 337 MET cc_start: 0.8560 (mtm) cc_final: 0.8006 (mtt) REVERT: a 364 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7605 (mppt) REVERT: a 424 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7632 (tt0) REVERT: b 247 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: b 266 LYS cc_start: 0.8839 (mmtp) cc_final: 0.8471 (mmtt) REVERT: b 364 LYS cc_start: 0.8136 (mttt) cc_final: 0.7861 (mppt) REVERT: b 445 ARG cc_start: 0.8545 (ttm110) cc_final: 0.8180 (mtp180) REVERT: c 216 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8578 (mp) REVERT: c 268 ARG cc_start: 0.8285 (ttp80) cc_final: 0.7996 (ttp-170) REVERT: c 292 LYS cc_start: 0.8340 (pttp) cc_final: 0.7955 (mmtm) REVERT: c 410 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6697 (ptpp) outliers start: 31 outliers final: 14 residues processed: 146 average time/residue: 1.4110 time to fit residues: 219.8011 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain C residue 57 LYS 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 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 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 76 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102257 restraints weight = 10624.219| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.77 r_work: 0.2973 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9858 Z= 0.135 Angle : 0.543 9.888 13395 Z= 0.277 Chirality : 0.044 0.177 1617 Planarity : 0.004 0.049 1689 Dihedral : 5.720 52.673 1545 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.61 % Allowed : 13.26 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1236 helix: 2.65 (0.22), residues: 534 sheet: 1.49 (0.47), residues: 111 loop : -0.86 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.017 0.001 TYR c 210 ARG 0.012 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00567 ( 9) link_NAG-ASN : angle 3.21355 ( 27) hydrogen bonds : bond 0.03975 ( 493) hydrogen bonds : angle 3.96690 ( 1410) SS BOND : bond 0.00295 ( 15) SS BOND : angle 1.82501 ( 30) covalent geometry : bond 0.00310 ( 9834) covalent geometry : angle 0.51766 (13338) *********************** 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 149 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.182 Fit side-chains REVERT: A 78 ARG cc_start: 0.8718 (ttp80) cc_final: 0.8204 (ttm-80) REVERT: A 81 ARG cc_start: 0.8116 (mtt-85) cc_final: 0.7817 (mtm110) REVERT: B 46 MET cc_start: 0.9214 (mtm) cc_final: 0.8980 (mtp) REVERT: C 57 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8370 (mmtt) REVERT: C 75 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8013 (mm-30) REVERT: C 85 GLU cc_start: 0.8547 (tp30) cc_final: 0.8231 (tp30) REVERT: a 292 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7717 (ptmm) REVERT: a 337 MET cc_start: 0.8536 (mtm) cc_final: 0.7984 (mtt) REVERT: a 364 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7621 (mppt) REVERT: a 424 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7577 (tm-30) REVERT: b 247 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: b 266 LYS cc_start: 0.8774 (mmtp) cc_final: 0.8419 (mmtt) REVERT: b 364 LYS cc_start: 0.8166 (mttt) cc_final: 0.7865 (mppt) REVERT: b 445 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8204 (mtp180) REVERT: c 268 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7973 (ttp-170) REVERT: c 292 LYS cc_start: 0.8337 (pttp) cc_final: 0.7970 (mmtm) REVERT: c 410 LYS cc_start: 0.7607 (mmtm) cc_final: 0.6712 (ptpp) outliers start: 28 outliers final: 13 residues processed: 136 average time/residue: 1.4938 time to fit residues: 215.5235 Evaluate side-chains 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS 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 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 60 optimal weight: 0.6980 chunk 110 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 49 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102584 restraints weight = 10550.520| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.84 r_work: 0.2991 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9858 Z= 0.141 Angle : 0.546 8.321 13395 Z= 0.278 Chirality : 0.044 0.345 1617 Planarity : 0.004 0.055 1689 Dihedral : 5.440 52.781 1545 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.52 % Allowed : 13.73 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1236 helix: 2.69 (0.22), residues: 534 sheet: 1.52 (0.47), residues: 111 loop : -0.87 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.013 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00499 ( 9) link_NAG-ASN : angle 3.15898 ( 27) hydrogen bonds : bond 0.03955 ( 493) hydrogen bonds : angle 3.96101 ( 1410) SS BOND : bond 0.00380 ( 15) SS BOND : angle 2.06005 ( 30) covalent geometry : bond 0.00328 ( 9834) covalent geometry : angle 0.51907 (13338) *********************** 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 146 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.244 Fit side-chains REVERT: A 78 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8059 (ttm-80) REVERT: A 81 ARG cc_start: 0.8029 (mtt-85) cc_final: 0.7650 (mtm110) REVERT: B 46 MET cc_start: 0.9229 (mtm) cc_final: 0.9006 (mtp) REVERT: C 57 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8319 (mmtt) REVERT: C 75 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7863 (mm-30) REVERT: C 85 GLU cc_start: 0.8565 (tp30) cc_final: 0.8212 (tp30) REVERT: a 292 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7579 (ptmm) REVERT: a 337 MET cc_start: 0.8519 (mtm) cc_final: 0.7937 (mtt) REVERT: a 364 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7523 (mppt) REVERT: a 424 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7413 (tm-30) REVERT: b 247 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: b 266 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8365 (mmtt) REVERT: b 364 LYS cc_start: 0.8131 (mttt) cc_final: 0.7793 (mppt) REVERT: b 445 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8049 (mtp180) REVERT: c 268 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7975 (ttp-170) REVERT: c 292 LYS cc_start: 0.8328 (pttp) cc_final: 0.7876 (mmtm) REVERT: c 410 LYS cc_start: 0.7518 (mmtm) cc_final: 0.6582 (ptpp) outliers start: 27 outliers final: 12 residues processed: 134 average time/residue: 1.4722 time to fit residues: 209.7934 Evaluate side-chains 130 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS 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 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 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 16 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 49 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101863 restraints weight = 10476.201| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.80 r_work: 0.2962 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9858 Z= 0.136 Angle : 0.552 11.755 13395 Z= 0.280 Chirality : 0.045 0.423 1617 Planarity : 0.004 0.058 1689 Dihedral : 5.407 52.811 1545 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.05 % Allowed : 14.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.24), residues: 1236 helix: 2.72 (0.22), residues: 534 sheet: 1.56 (0.48), residues: 111 loop : -0.84 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.017 0.001 TYR c 210 ARG 0.014 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00744 ( 9) link_NAG-ASN : angle 3.62971 ( 27) hydrogen bonds : bond 0.03850 ( 493) hydrogen bonds : angle 3.94777 ( 1410) SS BOND : bond 0.00416 ( 15) SS BOND : angle 2.04457 ( 30) covalent geometry : bond 0.00316 ( 9834) covalent geometry : angle 0.51956 (13338) *********************** 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 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.096 Fit side-chains REVERT: A 78 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8181 (ttm-80) REVERT: A 81 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7833 (mtm110) REVERT: B 46 MET cc_start: 0.9254 (mtm) cc_final: 0.9031 (mtp) REVERT: C 75 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7964 (mm-30) REVERT: C 85 GLU cc_start: 0.8584 (tp30) cc_final: 0.8254 (tp30) REVERT: a 292 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7678 (ptmm) REVERT: a 337 MET cc_start: 0.8514 (mtm) cc_final: 0.7969 (mtt) REVERT: a 364 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7615 (mppt) REVERT: a 424 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7579 (tm-30) REVERT: b 247 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: b 266 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8423 (mmtt) REVERT: b 364 LYS cc_start: 0.8152 (mttt) cc_final: 0.7872 (mppt) REVERT: b 445 ARG cc_start: 0.8470 (ttm110) cc_final: 0.8161 (mtp85) REVERT: c 268 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7929 (ttp-110) REVERT: c 292 LYS cc_start: 0.8306 (pttp) cc_final: 0.7940 (mmtm) REVERT: c 410 LYS cc_start: 0.7617 (mmtm) cc_final: 0.6729 (ptpp) outliers start: 22 outliers final: 13 residues processed: 132 average time/residue: 1.4747 time to fit residues: 206.5185 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 213 ILE 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 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 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.149859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.101778 restraints weight = 10541.076| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.80 r_work: 0.2961 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9858 Z= 0.136 Angle : 0.541 7.732 13395 Z= 0.278 Chirality : 0.044 0.220 1617 Planarity : 0.004 0.061 1689 Dihedral : 5.277 52.800 1545 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.87 % Allowed : 14.38 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.24), residues: 1236 helix: 2.74 (0.22), residues: 534 sheet: 1.57 (0.47), residues: 111 loop : -0.82 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.017 0.001 TYR c 210 ARG 0.014 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00430 ( 9) link_NAG-ASN : angle 2.80849 ( 27) hydrogen bonds : bond 0.03808 ( 493) hydrogen bonds : angle 3.93606 ( 1410) SS BOND : bond 0.00394 ( 15) SS BOND : angle 2.25892 ( 30) covalent geometry : bond 0.00317 ( 9834) covalent geometry : angle 0.51618 (13338) ********************** 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 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.093 Fit side-chains REVERT: A 78 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8180 (ttm-80) REVERT: A 81 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7822 (mtm110) REVERT: B 46 MET cc_start: 0.9251 (mtm) cc_final: 0.9023 (mtp) REVERT: C 75 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 85 GLU cc_start: 0.8588 (tp30) cc_final: 0.8254 (tp30) REVERT: a 266 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8365 (mmtp) REVERT: a 292 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7681 (ptmm) REVERT: a 337 MET cc_start: 0.8521 (mtm) cc_final: 0.7988 (mtt) REVERT: a 364 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7599 (mppt) REVERT: a 424 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7577 (tm-30) REVERT: b 247 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: b 266 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8379 (mmmt) REVERT: b 364 LYS cc_start: 0.8165 (mttt) cc_final: 0.7866 (mppt) REVERT: b 445 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8225 (mtp85) REVERT: c 268 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7937 (ttp-110) REVERT: c 292 LYS cc_start: 0.8298 (pttp) cc_final: 0.7941 (mmtm) REVERT: c 410 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6703 (ptpp) outliers start: 20 outliers final: 13 residues processed: 133 average time/residue: 1.5010 time to fit residues: 211.6669 Evaluate side-chains 132 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 213 ILE 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 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 117 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 383 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101679 restraints weight = 10491.884| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.80 r_work: 0.2957 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9858 Z= 0.146 Angle : 0.549 8.016 13395 Z= 0.282 Chirality : 0.044 0.371 1617 Planarity : 0.004 0.062 1689 Dihedral : 5.191 52.801 1545 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 14.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1236 helix: 2.72 (0.22), residues: 534 sheet: 1.56 (0.47), residues: 111 loop : -0.82 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.014 0.000 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 9) link_NAG-ASN : angle 2.92682 ( 27) hydrogen bonds : bond 0.03861 ( 493) hydrogen bonds : angle 3.94940 ( 1410) SS BOND : bond 0.00421 ( 15) SS BOND : angle 2.31337 ( 30) covalent geometry : bond 0.00344 ( 9834) covalent geometry : angle 0.52293 (13338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8278.55 seconds wall clock time: 142 minutes 57.90 seconds (8577.90 seconds total)