Starting phenix.real_space_refine on Thu Jan 16 18:53:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8utf_42539/01_2025/8utf_42539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8utf_42539/01_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_42539/01_2025/8utf_42539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8utf_42539/01_2025/8utf_42539.map" model { file = "/net/cci-nas-00/data/ceres_data/8utf_42539/01_2025/8utf_42539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8utf_42539/01_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-5571/modules/chem_data/mon_lib" Total number of atoms: 9827 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "B" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "C" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 565 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "a" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "b" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "c" Number of atoms: 2624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2624 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 13, 'TRANS': 330} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "a" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "b" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "c" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 7.88, per 1000 atoms: 0.80 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 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: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 26 through 32 removed outlier: 3.793A pdb=" N LYS A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 95 Proline residue: A 86 - end of helix Processing helix chain 'B' and resid 26 through 32 removed outlier: 3.778A pdb=" N LYS B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 95 Proline residue: B 86 - end of helix Processing helix chain 'C' and resid 30 through 33 removed outlier: 3.651A pdb=" N ILE C 33 " --> pdb=" O LEU C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 33' Processing helix chain 'C' and resid 69 through 95 Proline residue: C 86 - end of helix Processing helix chain 'a' and resid 142 through 185 removed outlier: 3.605A pdb=" N THR a 156 " --> pdb=" O ALA a 152 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE a 164 " --> pdb=" O ALA a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 223 removed outlier: 3.565A pdb=" N TYR a 210 " --> pdb=" O LEU a 206 " (cutoff:3.500A) Proline residue: a 219 - end of helix Processing helix chain 'a' and resid 230 through 238 Processing helix chain 'a' and resid 241 through 250 Processing helix chain 'a' and resid 253 through 263 removed outlier: 3.664A pdb=" N LEU a 257 " --> pdb=" O GLY a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 352 through 360 Processing helix chain 'a' and resid 362 through 366 Processing helix chain 'a' and resid 459 through 484 removed outlier: 4.823A pdb=" N ALA a 473 " --> pdb=" O LYS a 469 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS a 474 " --> pdb=" O LEU a 470 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU a 475 " --> pdb=" O GLU a 471 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU a 476 " --> pdb=" O ASP a 472 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER a 480 " --> pdb=" O LEU a 476 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP a 481 " --> pdb=" O LEU a 477 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN a 482 " --> pdb=" O GLU a 478 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE a 483 " --> pdb=" O SER a 479 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 186 Processing helix chain 'b' and resid 186 through 223 Proline residue: b 219 - end of helix Processing helix chain 'b' and resid 230 through 238 Processing helix chain 'b' and resid 241 through 250 Processing helix chain 'b' and resid 253 through 263 Processing helix chain 'b' and resid 352 through 360 Processing helix chain 'b' and resid 362 through 366 Processing helix chain 'b' and resid 459 through 484 removed outlier: 3.686A pdb=" N LEU b 463 " --> pdb=" O VAL b 459 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU b 478 " --> pdb=" O LYS b 474 " (cutoff:3.500A) Processing helix chain 'c' and resid 142 through 186 removed outlier: 3.544A pdb=" N THR c 157 " --> pdb=" O SER c 153 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 223 Proline residue: c 219 - end of helix Processing helix chain 'c' and resid 230 through 238 Processing helix chain 'c' and resid 241 through 250 Processing helix chain 'c' and resid 253 through 263 removed outlier: 3.618A pdb=" N LEU c 257 " --> pdb=" O GLY c 253 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 361 Processing helix chain 'c' and resid 362 through 366 Processing helix chain 'c' and resid 459 through 484 removed outlier: 3.590A pdb=" N LEU c 463 " --> pdb=" O VAL c 459 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE c 483 " --> pdb=" O SER c 479 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU c 484 " --> pdb=" O SER c 480 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 57 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 35 through 57 current: chain 'a' and resid 266 through 273 removed outlier: 3.776A pdb=" N LYS a 266 " --> pdb=" O ALA a 284 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL a 280 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N VAL a 272 " --> pdb=" O PHE a 278 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE a 278 " --> pdb=" O VAL a 272 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N TYR a 318 " --> pdb=" O PHE a 329 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE a 329 " --> pdb=" O TYR a 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 325 through 329 current: chain 'a' and resid 340 through 343 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.158A pdb=" N ASN A 61 " --> pdb=" O ILE c 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 35 through 37 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 35 through 37 current: chain 'a' and resid 440 through 442 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 440 through 442 current: chain 'b' and resid 266 through 273 removed outlier: 3.783A pdb=" N LYS b 266 " --> pdb=" O ALA b 284 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL b 280 " --> pdb=" O THR b 270 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL b 272 " --> pdb=" O PHE b 278 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE b 278 " --> pdb=" O VAL b 272 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N TYR b 318 " --> pdb=" O PHE b 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 329 " --> pdb=" O TYR b 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 325 through 329 current: chain 'b' and resid 341 through 343 Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.053A pdb=" N ASN B 61 " --> pdb=" O ILE a 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 57 removed outlier: 8.912A pdb=" N ALA b 440 " --> pdb=" O HIS C 51 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 53 " --> pdb=" O ALA b 440 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR b 442 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL C 55 " --> pdb=" O TYR b 442 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 440 through 442 current: chain 'c' and resid 266 through 273 removed outlier: 6.131A pdb=" N ALA c 267 " --> pdb=" O ALA c 284 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA c 284 " --> pdb=" O ALA c 267 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ILE c 269 " --> pdb=" O SER c 282 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER c 282 " --> pdb=" O ILE c 269 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS c 271 " --> pdb=" O VAL c 280 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR c 318 " --> pdb=" O PHE c 329 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE c 329 " --> pdb=" O TYR c 318 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 325 through 329 current: chain 'c' and resid 340 through 343 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 62 removed outlier: 5.745A pdb=" N ASN C 61 " --> pdb=" O ILE b 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'a' and resid 305 through 306 Processing sheet with id=AA8, first strand: chain 'a' and resid 379 through 382 Processing sheet with id=AA9, first strand: chain 'a' and resid 403 through 404 removed outlier: 4.471A pdb=" N CYS a 395 " --> pdb=" O ILE a 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 304 through 306 Processing sheet with id=AB2, first strand: chain 'b' and resid 379 through 382 Processing sheet with id=AB3, first strand: chain 'b' and resid 395 through 397 Processing sheet with id=AB4, first strand: chain 'c' and resid 304 through 306 removed outlier: 3.959A pdb=" N GLN c 309 " --> pdb=" O ILE c 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 379 through 382 Processing sheet with id=AB6, first strand: chain 'c' and resid 403 through 404 removed outlier: 4.468A pdb=" N CYS c 395 " --> pdb=" O ILE c 404 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.03 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3187 1.34 - 1.46: 1617 1.46 - 1.58: 4952 1.58 - 1.70: 0 1.70 - 1.81: 78 Bond restraints: 9834 Sorted by residual: bond pdb=" CG LEU c 206 " pdb=" CD1 LEU c 206 " ideal model delta sigma weight residual 1.521 1.497 0.024 3.30e-02 9.18e+02 5.20e-01 bond pdb=" CA VAL a 371 " pdb=" CB VAL a 371 " ideal model delta sigma weight residual 1.527 1.536 -0.009 1.31e-02 5.83e+03 4.99e-01 bond pdb=" CG LEU a 238 " pdb=" CD1 LEU a 238 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 4.88e-01 bond pdb=" CB LEU a 206 " pdb=" CG LEU a 206 " ideal model delta sigma weight residual 1.530 1.517 0.013 2.00e-02 2.50e+03 4.27e-01 bond pdb=" CG LEU a 457 " pdb=" CD2 LEU a 457 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.07e-01 ... (remaining 9829 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 13200 1.71 - 3.42: 115 3.42 - 5.13: 22 5.13 - 6.84: 0 6.84 - 8.55: 1 Bond angle restraints: 13338 Sorted by residual: angle pdb=" CA LEU a 206 " pdb=" CB LEU a 206 " pdb=" CG LEU a 206 " ideal model delta sigma weight residual 116.30 124.85 -8.55 3.50e+00 8.16e-02 5.96e+00 angle pdb=" CA GLN b 383 " pdb=" CB GLN b 383 " pdb=" CG GLN b 383 " ideal model delta sigma weight residual 114.10 117.38 -3.28 2.00e+00 2.50e-01 2.68e+00 angle pdb=" OG1 THR C 47 " pdb=" CB THR C 47 " pdb=" CG2 THR C 47 " ideal model delta sigma weight residual 109.30 106.04 3.26 2.00e+00 2.50e-01 2.66e+00 angle pdb=" C SER b 382 " pdb=" N GLN b 383 " pdb=" CA GLN b 383 " ideal model delta sigma weight residual 122.82 125.02 -2.20 1.42e+00 4.96e-01 2.40e+00 angle pdb=" CA TYR b 349 " pdb=" CB TYR b 349 " pdb=" CG TYR b 349 " ideal model delta sigma weight residual 113.90 116.62 -2.72 1.80e+00 3.09e-01 2.29e+00 ... (remaining 13333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 5731 22.30 - 44.59: 296 44.59 - 66.89: 78 66.89 - 89.19: 16 89.19 - 111.49: 20 Dihedral angle restraints: 6141 sinusoidal: 2547 harmonic: 3594 Sorted by residual: dihedral pdb=" CB CYS b 397 " pdb=" SG CYS b 397 " pdb=" SG CYS b 420 " pdb=" CB CYS b 420 " ideal model delta sinusoidal sigma weight residual -86.00 -130.75 44.75 1 1.00e+01 1.00e-02 2.78e+01 dihedral pdb=" CB CYS a 397 " pdb=" SG CYS a 397 " pdb=" SG CYS a 420 " pdb=" CB CYS a 420 " ideal model delta sinusoidal sigma weight residual -86.00 -129.14 43.14 1 1.00e+01 1.00e-02 2.59e+01 dihedral pdb=" CB CYS B 68 " pdb=" SG CYS B 68 " pdb=" SG CYS b 195 " pdb=" CB CYS b 195 " ideal model delta sinusoidal sigma weight residual -86.00 -125.90 39.90 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 6138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1227 0.041 - 0.081: 240 0.081 - 0.122: 132 0.122 - 0.163: 16 0.163 - 0.203: 2 Chirality restraints: 1617 Sorted by residual: chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL c 459 " pdb=" CA VAL c 459 " pdb=" CG1 VAL c 459 " pdb=" CG2 VAL c 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CB VAL a 459 " pdb=" CA VAL a 459 " pdb=" CG1 VAL a 459 " pdb=" CG2 VAL a 459 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.46e-01 ... (remaining 1614 not shown) Planarity restraints: 1698 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR b 349 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO b 350 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO b 350 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO b 350 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET c 337 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO c 338 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO c 338 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO c 338 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL c 315 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.14e+00 pdb=" N PRO c 316 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO c 316 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO c 316 " -0.015 5.00e-02 4.00e+02 ... (remaining 1695 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1386 2.76 - 3.29: 9254 3.29 - 3.83: 16096 3.83 - 4.36: 19964 4.36 - 4.90: 34264 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" OH TYR b 442 " pdb=" OE2 GLU c 212 " model vdw 2.222 3.040 nonbonded pdb=" O VAL b 302 " pdb=" O HOH b 601 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN b 346 " pdb=" O HOH b 602 " model vdw 2.253 3.040 nonbonded pdb=" OE2 GLU a 212 " pdb=" OH TYR c 442 " model vdw 2.260 3.040 nonbonded pdb=" O ILE a 411 " pdb=" O HOH a 601 " model vdw 2.262 3.040 ... (remaining 80959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.130 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.450 Find NCS groups from input model: 0.370 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:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.740 ------------------------------------------------------------------------------- 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 9834 Z= 0.180 Angle : 0.455 8.548 13338 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 *********************** 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 : 1.088 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: 1.4244 time to fit residues: 325.5110 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 : 1.595 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 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: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.148560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.101033 restraints weight = 10483.410| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.74 r_work: 0.2940 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 9834 Z= 0.348 Angle : 0.639 8.861 13338 Z= 0.327 Chirality : 0.049 0.348 1617 Planarity : 0.005 0.037 1689 Dihedral : 11.610 100.166 1549 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.68 % Allowed : 8.59 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.93 (0.23), residues: 1236 helix: 1.91 (0.21), residues: 531 sheet: 1.64 (0.46), residues: 114 loop : -0.83 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 311 HIS 0.006 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.021 0.002 TYR c 210 ARG 0.005 0.001 ARG b 263 *********************** 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 157 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.120 Fit side-chains REVERT: A 78 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8197 (ttm-80) REVERT: A 81 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7840 (mtm110) REVERT: B 46 MET cc_start: 0.9210 (mtm) cc_final: 0.8950 (mtp) REVERT: B 85 GLU cc_start: 0.8554 (tp30) cc_final: 0.8306 (tp30) REVERT: C 75 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7984 (mm-30) REVERT: C 85 GLU cc_start: 0.8706 (tp30) cc_final: 0.8298 (tp30) REVERT: a 292 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7764 (ptmm) REVERT: a 337 MET cc_start: 0.8556 (mtm) cc_final: 0.8067 (mtt) REVERT: a 364 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7730 (mppt) REVERT: b 266 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8466 (mmtt) REVERT: b 364 LYS cc_start: 0.8145 (mttt) cc_final: 0.7914 (mppt) REVERT: b 411 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7977 (mm) REVERT: b 445 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8215 (mtp180) REVERT: c 275 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: c 292 LYS cc_start: 0.8315 (pttp) cc_final: 0.7976 (mmtm) REVERT: c 410 LYS cc_start: 0.7645 (mmtm) cc_final: 0.6756 (ptpp) REVERT: c 435 ARG cc_start: 0.7977 (ttt90) cc_final: 0.7758 (ttt180) outliers start: 18 outliers final: 6 residues processed: 144 average time/residue: 1.5585 time to fit residues: 238.1115 Evaluate side-chains 136 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 275 GLU 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: 0.9990 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.148555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.100479 restraints weight = 10626.374| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.78 r_work: 0.2932 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9834 Z= 0.313 Angle : 0.609 8.131 13338 Z= 0.308 Chirality : 0.047 0.282 1617 Planarity : 0.005 0.054 1689 Dihedral : 8.666 65.773 1545 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.24 % Allowed : 10.18 % Favored : 87.58 % 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: 1.03 (0.23), residues: 1236 helix: 2.13 (0.22), residues: 534 sheet: 1.49 (0.48), residues: 111 loop : -0.88 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.005 0.001 HIS a 444 PHE 0.015 0.002 PHE c 278 TYR 0.021 0.002 TYR c 210 ARG 0.009 0.001 ARG a 445 *********************** 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 156 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8194 (ttm-80) REVERT: A 81 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7814 (mtm110) REVERT: B 46 MET cc_start: 0.9206 (mtm) cc_final: 0.8965 (mtp) REVERT: B 85 GLU cc_start: 0.8517 (tp30) cc_final: 0.8218 (tp30) REVERT: C 57 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8435 (mmtt) REVERT: C 75 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8044 (mm-30) REVERT: C 85 GLU cc_start: 0.8570 (tp30) cc_final: 0.8270 (tp30) REVERT: a 292 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7704 (ptmm) REVERT: a 337 MET cc_start: 0.8536 (mtm) cc_final: 0.8014 (mtt) REVERT: a 364 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7717 (mppt) REVERT: a 424 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7590 (tt0) REVERT: b 266 LYS cc_start: 0.8861 (mmtp) cc_final: 0.8475 (mmtt) REVERT: b 275 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: b 364 LYS cc_start: 0.8120 (mttt) cc_final: 0.7897 (mppt) REVERT: b 411 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (mm) REVERT: b 445 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8189 (mtp180) REVERT: c 292 LYS cc_start: 0.8323 (pttp) cc_final: 0.7962 (mmtm) REVERT: c 410 LYS cc_start: 0.7572 (mmtm) cc_final: 0.6739 (ptpp) REVERT: c 435 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7737 (ttt180) outliers start: 24 outliers final: 8 residues processed: 140 average time/residue: 1.5349 time to fit residues: 228.0347 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 : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain a residue 247 GLU Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 275 GLU Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 411 ILE Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain c residue 400 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.149521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102196 restraints weight = 10520.201| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.76 r_work: 0.2956 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9834 Z= 0.225 Angle : 0.547 7.240 13338 Z= 0.281 Chirality : 0.047 0.426 1617 Planarity : 0.004 0.044 1689 Dihedral : 6.468 51.981 1545 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.52 % Allowed : 11.30 % 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: 1.22 (0.24), residues: 1236 helix: 2.42 (0.22), residues: 531 sheet: 1.52 (0.47), residues: 111 loop : -0.90 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.009 0.001 ARG c 445 *********************** 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 150 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8191 (ttm-80) REVERT: A 81 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7884 (mtm110) REVERT: B 46 MET cc_start: 0.9199 (mtm) cc_final: 0.8958 (mtp) REVERT: B 85 GLU cc_start: 0.8454 (tp30) cc_final: 0.8157 (tp30) REVERT: C 75 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8014 (mm-30) REVERT: C 85 GLU cc_start: 0.8579 (tp30) cc_final: 0.8251 (tp30) REVERT: a 292 LYS cc_start: 0.8054 (mmtt) cc_final: 0.7704 (ptmm) REVERT: a 337 MET cc_start: 0.8457 (mtm) cc_final: 0.8037 (mtt) REVERT: a 364 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7655 (mppt) REVERT: a 424 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7599 (tt0) REVERT: b 247 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: b 266 LYS cc_start: 0.8834 (mmtp) cc_final: 0.8466 (mmtt) REVERT: b 275 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: b 364 LYS cc_start: 0.8122 (mttt) cc_final: 0.7903 (mppt) REVERT: b 445 ARG cc_start: 0.8519 (ttm110) cc_final: 0.8144 (mtp180) REVERT: c 268 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7974 (ttp-170) REVERT: c 292 LYS cc_start: 0.8330 (pttp) cc_final: 0.7970 (mmtm) REVERT: c 410 LYS cc_start: 0.7579 (mmtm) cc_final: 0.6710 (ptpp) REVERT: c 435 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7758 (ttt180) outliers start: 27 outliers final: 8 residues processed: 136 average time/residue: 1.5961 time to fit residues: 230.2273 Evaluate side-chains 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 98 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** b 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.150063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.102201 restraints weight = 10445.870| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.80 r_work: 0.2974 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9834 Z= 0.193 Angle : 0.509 6.942 13338 Z= 0.265 Chirality : 0.045 0.308 1617 Planarity : 0.004 0.042 1689 Dihedral : 5.752 55.223 1545 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.80 % Allowed : 11.48 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.24), residues: 1236 helix: 2.67 (0.22), residues: 528 sheet: 1.58 (0.48), residues: 111 loop : -0.88 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.010 0.000 ARG c 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 78 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8036 (ttm-80) REVERT: A 81 ARG cc_start: 0.8004 (mtt-85) cc_final: 0.7629 (mtm110) REVERT: B 46 MET cc_start: 0.9191 (mtm) cc_final: 0.8938 (mtp) REVERT: C 57 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8331 (mmtt) REVERT: C 75 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7882 (mm-30) REVERT: C 85 GLU cc_start: 0.8511 (tp30) cc_final: 0.8164 (tp30) REVERT: a 292 LYS cc_start: 0.8063 (mmtt) cc_final: 0.7610 (ptmm) REVERT: a 337 MET cc_start: 0.8432 (mtm) cc_final: 0.7964 (mtt) REVERT: a 364 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7523 (mppt) REVERT: a 424 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7373 (tm-30) REVERT: b 247 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: b 266 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8402 (mmtt) REVERT: b 364 LYS cc_start: 0.8149 (mttt) cc_final: 0.7797 (mppt) REVERT: b 445 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8078 (mtp180) REVERT: c 268 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7977 (ttp-170) REVERT: c 292 LYS cc_start: 0.8318 (pttp) cc_final: 0.7895 (mmtm) REVERT: c 410 LYS cc_start: 0.7496 (mmtm) cc_final: 0.6606 (ptpp) outliers start: 30 outliers final: 11 residues processed: 142 average time/residue: 1.4494 time to fit residues: 219.1487 Evaluate side-chains 133 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 396 LYS Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 418 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 27 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 120 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 406 GLN ** 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 = 0.3685 r_free = 0.3685 target = 0.148806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101699 restraints weight = 10618.749| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.75 r_work: 0.2949 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9834 Z= 0.270 Angle : 0.550 7.016 13338 Z= 0.286 Chirality : 0.046 0.402 1617 Planarity : 0.004 0.049 1689 Dihedral : 5.755 52.450 1545 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.52 % Allowed : 12.23 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.63 (0.22), residues: 528 sheet: 1.51 (0.47), residues: 111 loop : -0.90 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.014 0.002 PHE c 278 TYR 0.020 0.002 TYR c 210 ARG 0.010 0.001 ARG c 445 *********************** 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 149 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.172 Fit side-chains REVERT: A 78 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8189 (ttm-80) REVERT: A 81 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7814 (mtm110) REVERT: B 46 MET cc_start: 0.9237 (mtm) cc_final: 0.8998 (mtp) REVERT: C 57 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8346 (mmtt) REVERT: C 75 GLU cc_start: 0.8255 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 85 GLU cc_start: 0.8587 (tp30) cc_final: 0.8244 (tp30) REVERT: a 190 MET cc_start: 0.8292 (tpp) cc_final: 0.8051 (tpp) REVERT: a 292 LYS cc_start: 0.8068 (mmtt) cc_final: 0.7715 (ptmm) REVERT: a 337 MET cc_start: 0.8474 (mtm) cc_final: 0.8021 (mtt) REVERT: a 364 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7620 (mppt) REVERT: a 424 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7551 (tm-30) REVERT: b 247 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: b 266 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8470 (mmtt) REVERT: b 364 LYS cc_start: 0.8122 (mttt) cc_final: 0.7872 (mppt) REVERT: b 445 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8206 (mtp180) REVERT: c 216 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8593 (mp) REVERT: c 268 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7980 (ttp-170) REVERT: c 292 LYS cc_start: 0.8322 (pttp) cc_final: 0.7953 (mmtm) REVERT: c 410 LYS cc_start: 0.7600 (mmtm) cc_final: 0.6717 (ptpp) outliers start: 27 outliers final: 13 residues processed: 137 average time/residue: 1.4533 time to fit residues: 211.7720 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 : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASN Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 216 LEU Chi-restraints excluded: chain c residue 400 THR Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 47 optimal weight: 0.1980 chunk 43 optimal weight: 0.0980 chunk 76 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 117 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.151307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.103146 restraints weight = 10647.593| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.80 r_work: 0.2978 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9834 Z= 0.165 Angle : 0.495 7.167 13338 Z= 0.260 Chirality : 0.044 0.204 1617 Planarity : 0.004 0.045 1689 Dihedral : 5.399 52.703 1545 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.15 % Allowed : 13.17 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1236 helix: 2.72 (0.22), residues: 534 sheet: 1.67 (0.48), residues: 111 loop : -0.81 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.002 0.000 HIS a 444 PHE 0.013 0.001 PHE c 278 TYR 0.015 0.001 TYR c 210 ARG 0.011 0.000 ARG c 445 *********************** 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 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 1.112 Fit side-chains REVERT: A 78 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8160 (ttm-80) REVERT: A 81 ARG cc_start: 0.8094 (mtt-85) cc_final: 0.7815 (mtm110) REVERT: B 46 MET cc_start: 0.9239 (mtm) cc_final: 0.9004 (mtp) REVERT: C 57 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8316 (mmtt) REVERT: C 75 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7983 (mm-30) REVERT: C 85 GLU cc_start: 0.8533 (tp30) cc_final: 0.8219 (tp30) REVERT: C 89 ASP cc_start: 0.8399 (t0) cc_final: 0.8161 (t0) REVERT: a 247 GLU cc_start: 0.7766 (tt0) cc_final: 0.7490 (tm-30) REVERT: a 292 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7643 (ptmm) REVERT: a 337 MET cc_start: 0.8407 (mtm) cc_final: 0.7995 (mtt) REVERT: a 364 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7619 (mppt) REVERT: a 424 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7645 (tt0) REVERT: b 247 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: b 266 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8428 (mmtt) REVERT: b 364 LYS cc_start: 0.8102 (mttt) cc_final: 0.7861 (mppt) REVERT: b 445 ARG cc_start: 0.8596 (ttm110) cc_final: 0.8212 (mtp180) REVERT: c 268 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7940 (ttp-110) REVERT: c 292 LYS cc_start: 0.8319 (pttp) cc_final: 0.7947 (mmtm) REVERT: c 410 LYS cc_start: 0.7596 (mmtm) cc_final: 0.6697 (ptpp) outliers start: 23 outliers final: 10 residues processed: 133 average time/residue: 1.4866 time to fit residues: 210.4952 Evaluate side-chains 128 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 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 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 60 optimal weight: 0.4980 chunk 110 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.151671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.102697 restraints weight = 10542.354| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.85 r_work: 0.2993 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9834 Z= 0.234 Angle : 0.521 6.949 13338 Z= 0.274 Chirality : 0.044 0.274 1617 Planarity : 0.004 0.052 1689 Dihedral : 5.263 52.835 1545 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.77 % Allowed : 14.01 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1236 helix: 2.68 (0.22), residues: 537 sheet: 1.62 (0.47), residues: 111 loop : -0.82 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.018 0.001 TYR c 210 ARG 0.012 0.001 ARG c 445 *********************** 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 139 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.121 Fit side-chains REVERT: A 78 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8060 (ttm-80) REVERT: A 81 ARG cc_start: 0.8009 (mtt-85) cc_final: 0.7643 (mtm110) REVERT: B 46 MET cc_start: 0.9231 (mtm) cc_final: 0.8996 (mtp) REVERT: C 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 85 GLU cc_start: 0.8564 (tp30) cc_final: 0.8222 (tp30) REVERT: a 247 GLU cc_start: 0.7720 (tt0) cc_final: 0.7451 (tm-30) REVERT: a 292 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7595 (ptmm) REVERT: a 337 MET cc_start: 0.8453 (mtm) cc_final: 0.7903 (mtt) REVERT: a 364 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7529 (mppt) REVERT: a 424 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7503 (tt0) REVERT: b 247 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: b 266 LYS cc_start: 0.8803 (mmtp) cc_final: 0.8394 (mmtt) REVERT: b 364 LYS cc_start: 0.8112 (mttt) cc_final: 0.7788 (mppt) REVERT: b 445 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8075 (mtp180) REVERT: c 268 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7969 (ttp-110) REVERT: c 292 LYS cc_start: 0.8300 (pttp) cc_final: 0.7884 (mmtm) REVERT: c 410 LYS cc_start: 0.7500 (mmtm) cc_final: 0.6579 (ptpp) outliers start: 19 outliers final: 12 residues processed: 131 average time/residue: 1.5757 time to fit residues: 220.5592 Evaluate side-chains 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 195 CYS Chi-restraints excluded: chain b residue 247 GLU 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 461 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.151385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.102412 restraints weight = 10486.709| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.84 r_work: 0.2992 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9834 Z= 0.255 Angle : 0.536 6.667 13338 Z= 0.281 Chirality : 0.046 0.453 1617 Planarity : 0.004 0.058 1689 Dihedral : 5.497 52.948 1545 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.24 % Allowed : 13.73 % Favored : 84.03 % 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: 1.45 (0.24), residues: 1236 helix: 2.64 (0.22), residues: 537 sheet: 1.58 (0.47), residues: 111 loop : -0.83 (0.24), residues: 588 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 0.013 0.000 ARG c 445 *********************** 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 141 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.216 Fit side-chains REVERT: A 78 ARG cc_start: 0.8640 (ttp80) cc_final: 0.8070 (ttm-80) REVERT: A 81 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7664 (mtm110) REVERT: B 46 MET cc_start: 0.9230 (mtm) cc_final: 0.9000 (mtp) REVERT: C 75 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 85 GLU cc_start: 0.8568 (tp30) cc_final: 0.8221 (tp30) REVERT: a 247 GLU cc_start: 0.7728 (tt0) cc_final: 0.7448 (tm-30) REVERT: a 292 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7592 (ptmm) REVERT: a 337 MET cc_start: 0.8557 (mtm) cc_final: 0.7975 (mtt) REVERT: a 364 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7543 (mppt) REVERT: a 424 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7516 (tt0) REVERT: b 247 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: b 266 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8382 (mmtt) REVERT: b 364 LYS cc_start: 0.8104 (mttt) cc_final: 0.7789 (mppt) REVERT: b 445 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8057 (mtp85) REVERT: c 268 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7973 (ttp-170) REVERT: c 292 LYS cc_start: 0.8307 (pttp) cc_final: 0.7879 (mmtm) REVERT: c 410 LYS cc_start: 0.7530 (mmtm) cc_final: 0.6601 (ptpp) outliers start: 24 outliers final: 14 residues processed: 131 average time/residue: 1.5365 time to fit residues: 213.4490 Evaluate side-chains 131 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 195 CYS Chi-restraints excluded: chain b residue 213 ILE Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 26 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 120 optimal weight: 0.0030 chunk 22 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.150518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102097 restraints weight = 10527.644| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.82 r_work: 0.2966 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9834 Z= 0.206 Angle : 0.515 6.648 13338 Z= 0.271 Chirality : 0.044 0.194 1617 Planarity : 0.004 0.060 1689 Dihedral : 5.319 52.910 1545 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 14.47 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1236 helix: 2.71 (0.22), residues: 537 sheet: 1.63 (0.48), residues: 111 loop : -0.80 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.017 0.001 TYR c 210 ARG 0.014 0.000 ARG c 445 ********************** 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 137 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.135 Fit side-chains REVERT: A 78 ARG cc_start: 0.8674 (ttp80) cc_final: 0.8168 (ttm-80) REVERT: A 81 ARG cc_start: 0.8119 (mtt-85) cc_final: 0.7831 (mtm110) REVERT: B 46 MET cc_start: 0.9244 (mtm) cc_final: 0.9019 (mtp) REVERT: C 75 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 85 GLU cc_start: 0.8574 (tp30) cc_final: 0.8248 (tp30) REVERT: a 247 GLU cc_start: 0.7745 (tt0) cc_final: 0.7501 (tm-30) REVERT: a 292 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7679 (ptmm) REVERT: a 337 MET cc_start: 0.8530 (mtm) cc_final: 0.7993 (mtt) REVERT: a 364 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7613 (mppt) REVERT: a 424 GLU cc_start: 0.8361 (mt-10) cc_final: 0.7652 (tt0) REVERT: b 247 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: b 266 LYS cc_start: 0.8764 (mmtp) cc_final: 0.8410 (mmtt) REVERT: b 364 LYS cc_start: 0.8164 (mttt) cc_final: 0.7866 (mppt) REVERT: b 445 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8199 (mtp85) REVERT: c 268 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7920 (ttp-110) REVERT: c 292 LYS cc_start: 0.8308 (pttp) cc_final: 0.7932 (mmtm) REVERT: c 410 LYS cc_start: 0.7619 (mmtm) cc_final: 0.6741 (ptpp) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 1.5113 time to fit residues: 206.9915 Evaluate side-chains 130 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 371 VAL Chi-restraints excluded: chain a residue 400 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain a residue 457 LEU Chi-restraints excluded: chain b residue 173 LEU Chi-restraints excluded: chain b residue 195 CYS Chi-restraints excluded: chain b residue 213 ILE Chi-restraints excluded: chain b residue 247 GLU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 341 THR Chi-restraints excluded: chain b residue 400 THR Chi-restraints excluded: chain b residue 419 HIS Chi-restraints excluded: chain b residue 461 THR Chi-restraints excluded: chain c residue 213 ILE Chi-restraints excluded: chain c residue 461 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 117 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.150411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102063 restraints weight = 10493.989| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.81 r_work: 0.2968 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9834 Z= 0.212 Angle : 0.514 6.280 13338 Z= 0.272 Chirality : 0.044 0.220 1617 Planarity : 0.004 0.061 1689 Dihedral : 5.219 52.828 1545 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.68 % Allowed : 14.85 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1236 helix: 2.70 (0.22), residues: 537 sheet: 1.63 (0.47), residues: 111 loop : -0.80 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.004 0.001 HIS a 444 PHE 0.013 0.002 PHE c 278 TYR 0.017 0.001 TYR c 210 ARG 0.014 0.000 ARG c 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8110.19 seconds wall clock time: 143 minutes 53.89 seconds (8633.89 seconds total)