Starting phenix.real_space_refine on Sun Jun 8 18:33:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utf_42539/06_2025/8utf_42539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utf_42539/06_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_42539/06_2025/8utf_42539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utf_42539/06_2025/8utf_42539.map" model { file = "/net/cci-nas-00/data/ceres_data/8utf_42539/06_2025/8utf_42539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utf_42539/06_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-5710/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: 6.83, per 1000 atoms: 0.70 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: 2.20 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: 1.00 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: 2.87 Time building geometry restraints manager: 2.65 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.860 Find NCS groups from input model: 0.360 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:14.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.280 ------------------------------------------------------------------------------- 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 : 1.106 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: 1.3923 time to fit residues: 318.2812 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 : 1.158 ------------------------------------------------------------------------------- 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 = 57)----------------| | 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: 0.8389 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 : 1.146 Fit side-chains REVERT: A 78 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8186 (ttm-80) REVERT: A 81 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7804 (mtm110) REVERT: B 46 MET cc_start: 0.9203 (mtm) cc_final: 0.8947 (mtp) REVERT: B 85 GLU cc_start: 0.8554 (tp30) cc_final: 0.8307 (tp30) REVERT: C 75 GLU cc_start: 0.8235 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 85 GLU cc_start: 0.8698 (tp30) cc_final: 0.8283 (tp30) REVERT: a 171 MET cc_start: 0.8032 (mtm) cc_final: 0.7827 (mtp) REVERT: a 292 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7761 (ptmm) REVERT: a 337 MET cc_start: 0.8542 (mtm) cc_final: 0.8037 (mtt) REVERT: a 364 LYS cc_start: 0.8110 (mmmt) cc_final: 0.7728 (mppt) REVERT: a 424 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7616 (tt0) REVERT: b 266 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8466 (mmtt) REVERT: b 364 LYS cc_start: 0.8154 (mttt) cc_final: 0.7916 (mppt) REVERT: b 411 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7956 (mm) REVERT: b 445 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8201 (mtp180) REVERT: c 292 LYS cc_start: 0.8314 (pttp) cc_final: 0.7973 (mmtm) REVERT: c 410 LYS cc_start: 0.7648 (mmtm) cc_final: 0.6746 (ptpp) REVERT: c 435 ARG cc_start: 0.7965 (ttt90) cc_final: 0.7739 (ttt180) outliers start: 17 outliers final: 6 residues processed: 143 average time/residue: 1.5914 time to fit residues: 241.7452 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 : 1.186 ------------------------------------------------------------------------------- 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: 7.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3679 r_free = 0.3679 target = 0.148350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100901 restraints weight = 10670.687| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.75 r_work: 0.2940 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9858 Z= 0.180 Angle : 0.602 7.641 13395 Z= 0.300 Chirality : 0.046 0.270 1617 Planarity : 0.005 0.047 1689 Dihedral : 7.861 61.392 1545 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 10.55 % Favored : 87.30 % 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: 1.13 (0.23), residues: 1236 helix: 2.29 (0.22), residues: 531 sheet: 1.52 (0.48), residues: 111 loop : -0.89 (0.24), residues: 594 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 0.015 0.002 PHE c 278 TYR 0.019 0.002 TYR c 210 ARG 0.009 0.001 ARG a 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00972 ( 9) link_NAG-ASN : angle 2.68770 ( 27) hydrogen bonds : bond 0.05080 ( 493) hydrogen bonds : angle 4.28731 ( 1410) SS BOND : bond 0.00382 ( 15) SS BOND : angle 1.67754 ( 30) covalent geometry : bond 0.00419 ( 9834) covalent geometry : angle 0.58541 (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 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8187 (ttm-80) REVERT: A 81 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7814 (mtm110) REVERT: B 46 MET cc_start: 0.9208 (mtm) cc_final: 0.8963 (mtp) REVERT: B 85 GLU cc_start: 0.8494 (tp30) cc_final: 0.8199 (tp30) REVERT: C 57 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8391 (mmtt) REVERT: C 75 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8027 (mm-30) REVERT: a 292 LYS cc_start: 0.8049 (mmtt) cc_final: 0.7706 (ptmm) REVERT: a 337 MET cc_start: 0.8518 (mtm) cc_final: 0.8009 (mtt) REVERT: a 364 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7739 (mppt) REVERT: a 424 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7596 (tt0) REVERT: b 266 LYS cc_start: 0.8845 (mmtp) cc_final: 0.8472 (mmtt) REVERT: b 275 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: b 364 LYS cc_start: 0.8112 (mttt) cc_final: 0.7893 (mppt) REVERT: b 445 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8211 (mtp180) REVERT: c 292 LYS cc_start: 0.8317 (pttp) cc_final: 0.7975 (mmtm) REVERT: c 410 LYS cc_start: 0.7581 (mmtm) cc_final: 0.6724 (ptpp) REVERT: c 435 ARG cc_start: 0.7979 (ttt90) cc_final: 0.7734 (ttt180) outliers start: 23 outliers final: 9 residues processed: 143 average time/residue: 1.5803 time to fit residues: 241.2304 Evaluate side-chains 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100307 restraints weight = 10489.824| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.81 r_work: 0.2933 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9858 Z= 0.195 Angle : 0.596 9.036 13395 Z= 0.301 Chirality : 0.047 0.407 1617 Planarity : 0.005 0.047 1689 Dihedral : 6.192 52.181 1545 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 11.48 % Favored : 86.18 % 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: 1.20 (0.24), residues: 1236 helix: 2.45 (0.22), residues: 531 sheet: 1.43 (0.47), residues: 111 loop : -0.93 (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 0.014 0.002 PHE c 278 TYR 0.021 0.002 TYR c 210 ARG 0.009 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.01389 ( 9) link_NAG-ASN : angle 2.72526 ( 27) hydrogen bonds : bond 0.04756 ( 493) hydrogen bonds : angle 4.20225 ( 1410) SS BOND : bond 0.00383 ( 15) SS BOND : angle 1.54170 ( 30) covalent geometry : bond 0.00460 ( 9834) covalent geometry : angle 0.57975 (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 154 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 1.050 Fit side-chains REVERT: A 78 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8177 (ttm-80) REVERT: A 81 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7823 (mtm110) REVERT: B 46 MET cc_start: 0.9229 (mtm) cc_final: 0.8996 (mtp) REVERT: B 85 GLU cc_start: 0.8432 (tp30) cc_final: 0.8093 (tp30) REVERT: C 75 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8026 (mm-30) REVERT: a 292 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7756 (ptmm) REVERT: a 337 MET cc_start: 0.8507 (mtm) cc_final: 0.8000 (mtt) REVERT: a 364 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7604 (mppt) REVERT: a 424 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7592 (tt0) REVERT: b 266 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8463 (mmtt) REVERT: b 275 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: b 364 LYS cc_start: 0.8147 (mttt) cc_final: 0.7882 (mppt) REVERT: b 445 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8144 (mtp180) REVERT: c 292 LYS cc_start: 0.8326 (pttp) cc_final: 0.7953 (mmtm) REVERT: c 410 LYS cc_start: 0.7583 (mmtm) cc_final: 0.6679 (ptpp) outliers start: 25 outliers final: 11 residues processed: 140 average time/residue: 1.4319 time to fit residues: 213.1880 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 275 GLU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 418 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.149197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102098 restraints weight = 10515.904| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.75 r_work: 0.2957 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9858 Z= 0.146 Angle : 0.542 7.241 13395 Z= 0.277 Chirality : 0.045 0.306 1617 Planarity : 0.004 0.044 1689 Dihedral : 5.648 52.302 1545 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 11.86 % Favored : 85.43 % 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: 1.34 (0.24), residues: 1236 helix: 2.61 (0.22), residues: 531 sheet: 1.50 (0.47), 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 0.004 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.009 0.000 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 9) link_NAG-ASN : angle 2.25341 ( 27) hydrogen bonds : bond 0.04249 ( 493) hydrogen bonds : angle 4.05059 ( 1410) SS BOND : bond 0.00377 ( 15) SS BOND : angle 1.64075 ( 30) covalent geometry : bond 0.00336 ( 9834) covalent geometry : angle 0.52760 (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 152 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.877 Fit side-chains REVERT: A 78 ARG cc_start: 0.8701 (ttp80) cc_final: 0.8200 (ttm-80) REVERT: A 81 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7831 (mtm110) REVERT: B 46 MET cc_start: 0.9226 (mtm) cc_final: 0.8990 (mtp) REVERT: C 57 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8328 (mmtt) REVERT: C 75 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7995 (mm-30) REVERT: a 292 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7716 (ptmm) REVERT: a 337 MET cc_start: 0.8464 (mtm) cc_final: 0.8086 (mtt) REVERT: a 364 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7625 (mppt) REVERT: a 424 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7532 (tm-30) REVERT: b 247 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: b 266 LYS cc_start: 0.8834 (mmtp) cc_final: 0.8471 (mmtt) REVERT: b 364 LYS cc_start: 0.8109 (mttt) cc_final: 0.7879 (mppt) REVERT: b 445 ARG cc_start: 0.8647 (ttm110) cc_final: 0.8222 (mtp180) REVERT: c 268 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7961 (ttp-170) REVERT: c 292 LYS cc_start: 0.8299 (pttp) cc_final: 0.7957 (mmtm) REVERT: c 410 LYS cc_start: 0.7599 (mmtm) cc_final: 0.6710 (ptpp) outliers start: 29 outliers final: 12 residues processed: 139 average time/residue: 1.4532 time to fit residues: 215.9306 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 : 1.031 ------------------------------------------------------------------------------- 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: 1.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 120 optimal weight: 0.0060 chunk 85 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.148989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.101056 restraints weight = 10536.252| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.77 r_work: 0.2955 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9858 Z= 0.183 Angle : 0.579 10.011 13395 Z= 0.294 Chirality : 0.046 0.392 1617 Planarity : 0.004 0.049 1689 Dihedral : 5.653 52.500 1545 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.80 % Allowed : 12.32 % Favored : 84.87 % 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: 2.63 (0.22), residues: 528 sheet: 1.48 (0.47), residues: 111 loop : -0.93 (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 0.00786 ( 9) link_NAG-ASN : angle 3.23929 ( 27) hydrogen bonds : bond 0.04375 ( 493) hydrogen bonds : angle 4.07256 ( 1410) SS BOND : bond 0.00467 ( 15) SS BOND : angle 1.86431 ( 30) covalent geometry : bond 0.00439 ( 9834) covalent geometry : angle 0.55510 (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 158 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 1.248 Fit side-chains REVERT: A 78 ARG cc_start: 0.8675 (ttp80) cc_final: 0.8146 (ttm-80) REVERT: A 81 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7769 (mtm110) REVERT: C 57 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8305 (mmtt) REVERT: C 75 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7996 (mm-30) REVERT: a 190 MET cc_start: 0.8321 (tpp) cc_final: 0.8070 (tpp) REVERT: a 292 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7695 (ptmm) REVERT: a 337 MET cc_start: 0.8514 (mtm) cc_final: 0.8088 (mtt) REVERT: a 364 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7607 (mppt) REVERT: a 424 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7581 (tt0) REVERT: b 171 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7441 (ttp) REVERT: b 247 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7402 (tm-30) REVERT: b 266 LYS cc_start: 0.8830 (mmtp) cc_final: 0.8449 (mmtt) REVERT: b 364 LYS cc_start: 0.8153 (mttt) cc_final: 0.7848 (mppt) REVERT: b 445 ARG cc_start: 0.8508 (ttm110) cc_final: 0.8140 (mtp180) REVERT: c 216 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8575 (mp) REVERT: c 268 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8003 (ttp-170) REVERT: c 292 LYS cc_start: 0.8320 (pttp) cc_final: 0.7940 (mmtm) REVERT: c 410 LYS cc_start: 0.7580 (mmtm) cc_final: 0.6656 (ptpp) outliers start: 30 outliers final: 14 residues processed: 145 average time/residue: 1.4051 time to fit residues: 217.8692 Evaluate side-chains 140 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 a residue 457 LEU Chi-restraints excluded: chain b residue 171 MET Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.149791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.101116 restraints weight = 10569.268| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.83 r_work: 0.2973 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9858 Z= 0.197 Angle : 0.593 10.275 13395 Z= 0.300 Chirality : 0.046 0.202 1617 Planarity : 0.004 0.051 1689 Dihedral : 5.758 52.708 1545 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 13.82 % 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: 1.29 (0.24), residues: 1236 helix: 2.61 (0.22), residues: 528 sheet: 1.38 (0.47), residues: 111 loop : -0.94 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 27 HIS 0.005 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.019 0.002 TYR b 210 ARG 0.011 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 9) link_NAG-ASN : angle 3.43123 ( 27) hydrogen bonds : bond 0.04418 ( 493) hydrogen bonds : angle 4.08991 ( 1410) SS BOND : bond 0.00418 ( 15) SS BOND : angle 2.01129 ( 30) covalent geometry : bond 0.00475 ( 9834) covalent geometry : angle 0.56616 (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 151 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.143 Fit side-chains REVERT: A 78 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8076 (ttm-80) REVERT: A 81 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7700 (mtm110) REVERT: C 57 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8322 (mmtt) REVERT: C 75 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7908 (mm-30) REVERT: a 292 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7700 (ptmm) REVERT: a 337 MET cc_start: 0.8523 (mtm) cc_final: 0.8061 (mtt) REVERT: a 364 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7539 (mppt) REVERT: a 424 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7474 (tt0) REVERT: b 247 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: b 266 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8417 (mmtt) REVERT: b 364 LYS cc_start: 0.8125 (mttt) cc_final: 0.7784 (mppt) REVERT: b 445 ARG cc_start: 0.8492 (ttm110) cc_final: 0.8066 (mtp180) REVERT: c 216 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8501 (mp) REVERT: c 268 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7991 (ttp-170) REVERT: c 292 LYS cc_start: 0.8301 (pttp) cc_final: 0.7888 (mmtm) REVERT: c 410 LYS cc_start: 0.7527 (mmtm) cc_final: 0.6612 (ptpp) outliers start: 25 outliers final: 13 residues processed: 139 average time/residue: 1.4803 time to fit residues: 218.6525 Evaluate side-chains 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 60 optimal weight: 0.5980 chunk 110 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.150028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.101673 restraints weight = 10530.257| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.87 r_work: 0.2981 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 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 : 0.004 0.041 9858 Z= 0.153 Angle : 0.563 8.281 13395 Z= 0.287 Chirality : 0.045 0.362 1617 Planarity : 0.004 0.053 1689 Dihedral : 5.497 52.747 1545 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 13.82 % 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: 1.34 (0.24), residues: 1236 helix: 2.62 (0.22), residues: 534 sheet: 1.41 (0.47), residues: 111 loop : -0.91 (0.24), residues: 591 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 0.012 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 3.20411 ( 27) hydrogen bonds : bond 0.04102 ( 493) hydrogen bonds : angle 4.02189 ( 1410) SS BOND : bond 0.00436 ( 15) SS BOND : angle 2.10064 ( 30) covalent geometry : bond 0.00358 ( 9834) covalent geometry : angle 0.53679 (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: 25 poor density : 121 time to evaluate : 1.051 Fit side-chains REVERT: A 78 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8027 (ttm-80) REVERT: A 81 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7694 (mtm110) REVERT: C 57 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8299 (mmtt) REVERT: C 75 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7840 (mm-30) REVERT: a 190 MET cc_start: 0.8333 (tpp) cc_final: 0.8056 (tpp) REVERT: a 292 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7671 (ptmm) REVERT: a 337 MET cc_start: 0.8552 (mtm) cc_final: 0.7961 (mtt) REVERT: a 364 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7496 (mppt) REVERT: a 424 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7322 (tm-30) REVERT: b 247 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: b 266 LYS cc_start: 0.8772 (mmtp) cc_final: 0.8362 (mmtt) REVERT: b 364 LYS cc_start: 0.8099 (mttt) cc_final: 0.7755 (mppt) REVERT: b 445 ARG cc_start: 0.8512 (ttm110) cc_final: 0.8027 (mtp180) REVERT: c 216 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8432 (mp) REVERT: c 268 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7956 (ttp-170) REVERT: c 292 LYS cc_start: 0.8310 (pttp) cc_final: 0.7857 (mmtm) REVERT: c 410 LYS cc_start: 0.7500 (mmtm) cc_final: 0.6556 (ptpp) outliers start: 25 outliers final: 13 residues processed: 137 average time/residue: 1.4902 time to fit residues: 217.8696 Evaluate side-chains 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.100960 restraints weight = 10498.294| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.79 r_work: 0.2947 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9858 Z= 0.162 Angle : 0.573 10.933 13395 Z= 0.291 Chirality : 0.045 0.409 1617 Planarity : 0.004 0.052 1689 Dihedral : 5.458 52.729 1545 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.24 % Allowed : 14.19 % Favored : 83.57 % 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: 1.35 (0.24), residues: 1236 helix: 2.63 (0.22), residues: 534 sheet: 1.39 (0.47), residues: 111 loop : -0.91 (0.24), residues: 591 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 0.019 0.001 TYR c 210 ARG 0.014 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00720 ( 9) link_NAG-ASN : angle 3.60498 ( 27) hydrogen bonds : bond 0.04106 ( 493) hydrogen bonds : angle 4.02145 ( 1410) SS BOND : bond 0.00376 ( 15) SS BOND : angle 2.31078 ( 30) covalent geometry : bond 0.00385 ( 9834) covalent geometry : angle 0.53997 (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 145 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 1.140 Fit side-chains REVERT: A 78 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8192 (ttm-80) REVERT: A 81 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7896 (mtm110) REVERT: C 57 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8324 (mmtt) REVERT: C 75 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7990 (mm-30) REVERT: a 292 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7795 (ptmm) REVERT: a 337 MET cc_start: 0.8572 (mtm) cc_final: 0.8018 (mtt) REVERT: a 364 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7607 (mppt) REVERT: a 424 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7588 (tm-30) REVERT: b 247 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: b 266 LYS cc_start: 0.8805 (mmtp) cc_final: 0.8453 (mmtt) REVERT: b 364 LYS cc_start: 0.8181 (mttt) cc_final: 0.7874 (mppt) REVERT: b 445 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8180 (mtp85) REVERT: c 216 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8587 (mp) REVERT: c 247 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: c 268 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7944 (ttp-170) REVERT: c 292 LYS cc_start: 0.8296 (pttp) cc_final: 0.7945 (mmtm) REVERT: c 410 LYS cc_start: 0.7614 (mmtm) cc_final: 0.6715 (ptpp) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 1.5346 time to fit residues: 220.0777 Evaluate side-chains 137 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 216 LEU Chi-restraints excluded: chain c residue 247 GLU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 457 LEU Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 4 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: ** 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 = 0.3688 r_free = 0.3688 target = 0.148843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.100496 restraints weight = 10546.886| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.79 r_work: 0.2939 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9858 Z= 0.179 Angle : 0.580 9.001 13395 Z= 0.298 Chirality : 0.045 0.243 1617 Planarity : 0.004 0.062 1689 Dihedral : 5.373 52.713 1545 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.05 % Allowed : 14.57 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.24), residues: 1236 helix: 2.60 (0.22), residues: 534 sheet: 1.36 (0.47), residues: 111 loop : -0.90 (0.24), residues: 591 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 0.019 0.002 TYR c 210 ARG 0.014 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 9) link_NAG-ASN : angle 2.91438 ( 27) hydrogen bonds : bond 0.04183 ( 493) hydrogen bonds : angle 4.06820 ( 1410) SS BOND : bond 0.00470 ( 15) SS BOND : angle 2.59102 ( 30) covalent geometry : bond 0.00429 ( 9834) covalent geometry : angle 0.55321 (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 145 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.002 Fit side-chains REVERT: A 78 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8193 (ttm-80) REVERT: A 81 ARG cc_start: 0.8157 (mtt-85) cc_final: 0.7840 (mtm110) REVERT: C 57 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8324 (mmtt) REVERT: C 75 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7992 (mm-30) REVERT: a 292 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7796 (ptmm) REVERT: a 337 MET cc_start: 0.8577 (mtm) cc_final: 0.8002 (mtt) REVERT: a 364 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7589 (mppt) REVERT: a 424 GLU cc_start: 0.8389 (mt-10) cc_final: 0.7561 (tm-30) REVERT: b 247 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: b 266 LYS cc_start: 0.8838 (mmtp) cc_final: 0.8483 (mmtt) REVERT: b 364 LYS cc_start: 0.8165 (mttt) cc_final: 0.7873 (mppt) REVERT: b 445 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8191 (mtp180) REVERT: c 216 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8573 (mp) REVERT: c 247 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: c 268 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7956 (ttp-170) REVERT: c 292 LYS cc_start: 0.8290 (pttp) cc_final: 0.7949 (mmtm) REVERT: c 339 GLU cc_start: 0.7745 (pm20) cc_final: 0.7137 (pm20) REVERT: c 410 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6718 (ptpp) outliers start: 22 outliers final: 14 residues processed: 136 average time/residue: 1.4318 time to fit residues: 206.6929 Evaluate side-chains 138 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 216 LEU Chi-restraints excluded: chain c residue 247 GLU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 457 LEU Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.149281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101011 restraints weight = 10505.376| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.80 r_work: 0.2946 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9858 Z= 0.164 Angle : 0.594 11.526 13395 Z= 0.299 Chirality : 0.045 0.440 1617 Planarity : 0.004 0.061 1689 Dihedral : 5.287 52.714 1545 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.33 % Allowed : 14.47 % Favored : 83.19 % 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: 1.35 (0.24), residues: 1236 helix: 2.64 (0.22), residues: 531 sheet: 1.39 (0.48), residues: 111 loop : -0.89 (0.24), residues: 594 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 0.014 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.014 0.001 ARG c 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 9) link_NAG-ASN : angle 4.36966 ( 27) hydrogen bonds : bond 0.04058 ( 493) hydrogen bonds : angle 4.03974 ( 1410) SS BOND : bond 0.00468 ( 15) SS BOND : angle 2.51420 ( 30) covalent geometry : bond 0.00388 ( 9834) covalent geometry : angle 0.54862 (13338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8712.39 seconds wall clock time: 150 minutes 49.61 seconds (9049.61 seconds total)