Starting phenix.real_space_refine on Thu Feb 5 02:44:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622.map" model { file = "/net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ev8_28622/02_2026/8ev8_28622_neut.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 66 5.16 5 C 9609 2.51 5 N 2401 2.21 5 O 2668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 187 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14748 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3675 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 449, 3664 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 14, 'TRANS': 434} Chain breaks: 1 bond proxies already assigned to first conformer: 3733 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3632 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 14, 'TRANS': 430} Chain breaks: 1 Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3697 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3610 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} Conformer: "B" Number of residues, atoms: 441, 3602 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 13, 'TRANS': 427} bond proxies already assigned to first conformer: 3684 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'NAG': 1, 'PCG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE A 392 " occ=0.70 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.30 Time building chain proxies: 4.51, per 1000 atoms: 0.31 Number of scatterers: 14748 At special positions: 0 Unit cell: (107.9, 112.88, 131.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 4 15.00 O 2668 8.00 N 2401 7.00 C 9609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 801 " - " ASN A 339 " " NAG B 801 " - " ASN B 339 " " NAG C 801 " - " ASN C 339 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 893.2 milliseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3394 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 12 sheets defined 66.7% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 166 through 193 Proline residue: A 178 - end of helix removed outlier: 3.864A pdb=" N ASP A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.755A pdb=" N TYR A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 255 removed outlier: 3.804A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.753A pdb=" N VAL A 273 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 275 " --> pdb=" O GLU A 272 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 278 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.109A pdb=" N LEU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 329 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 374 through 407 Processing helix chain 'A' and resid 407 through 427 Processing helix chain 'A' and resid 430 through 447 Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 487 through 497 Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.689A pdb=" N ILE A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 591 through 610 Processing helix chain 'B' and resid 165 through 193 removed outlier: 3.856A pdb=" N TYR B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.815A pdb=" N ASP B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.941A pdb=" N LYS B 250 " --> pdb=" O THR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.917A pdb=" N VAL B 273 " --> pdb=" O TYR B 270 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN B 276 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 278 " --> pdb=" O PHE B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.218A pdb=" N LEU B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 329 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 407 Processing helix chain 'B' and resid 407 through 427 Processing helix chain 'B' and resid 430 through 447 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 461 through 478 removed outlier: 6.164A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR B 476 " --> pdb=" O VAL B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 497 Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.945A pdb=" N TYR C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.816A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.986A pdb=" N LYS C 250 " --> pdb=" O THR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.957A pdb=" N VAL C 273 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN C 276 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 278 " --> pdb=" O PHE C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.957A pdb=" N LEU C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 329 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 374 through 407 removed outlier: 3.657A pdb=" N ASN C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 427 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 478 removed outlier: 6.088A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N THR C 476 " --> pdb=" O VAL C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 497 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'D' and resid 215 through 242 Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 271 removed outlier: 3.592A pdb=" N TRP D 253 " --> pdb=" O ASN D 249 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 275 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 297 through 307 removed outlier: 4.156A pdb=" N GLN D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 3.817A pdb=" N ILE D 312 " --> pdb=" O PRO D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 313 through 318 Processing helix chain 'D' and resid 324 through 329 removed outlier: 3.719A pdb=" N MET D 328 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 345 removed outlier: 4.178A pdb=" N PHE D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.377A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 490 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 521 removed outlier: 3.618A pdb=" N VAL D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ILE D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 646 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 228 Processing sheet with id=AA2, first strand: chain 'A' and resid 499 through 503 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 510 removed outlier: 6.888A pdb=" N ILE A 568 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL A 539 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 503 Processing sheet with id=AA6, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.598A pdb=" N TYR B 508 " --> pdb=" O SER B 570 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER B 570 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 510 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 527 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL B 540 " --> pdb=" O LEU B 527 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 529 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 227 through 228 Processing sheet with id=AA8, first strand: chain 'C' and resid 499 through 502 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 6.463A pdb=" N TYR C 508 " --> pdb=" O SER C 570 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER C 570 " --> pdb=" O TYR C 508 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS C 510 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 277 through 279 removed outlier: 4.034A pdb=" N PHE D 277 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP D 282 " --> pdb=" O ARG D 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545 Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 6.543A pdb=" N PHE D 550 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 610 " --> pdb=" O PHE D 550 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2724 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: 2.42 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4546 1.34 - 1.46: 3082 1.46 - 1.58: 7369 1.58 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 15102 Sorted by residual: bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.44e+01 bond pdb=" O5' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.489 0.117 2.00e-02 2.50e+03 3.39e+01 bond pdb=" O5' PCG B 802 " pdb=" PA PCG B 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " ideal model delta sigma weight residual 1.617 1.513 0.104 2.00e-02 2.50e+03 2.70e+01 ... (remaining 15097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 20371 3.66 - 7.32: 84 7.32 - 10.98: 34 10.98 - 14.64: 4 14.64 - 18.30: 12 Bond angle restraints: 20505 Sorted by residual: angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.15 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C3' PCG B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.11 -18.26 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG A 802 " pdb=" C4' PCG A 802 " pdb=" C5' PCG A 802 " ideal model delta sigma weight residual 109.85 128.10 -18.25 3.00e+00 1.11e-01 3.70e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.06 -18.21 3.00e+00 1.11e-01 3.69e+01 angle pdb=" O1A PCG A 802 " pdb=" PA PCG A 802 " pdb=" O5' PCG A 802 " ideal model delta sigma weight residual 102.28 118.01 -15.73 3.00e+00 1.11e-01 2.75e+01 ... (remaining 20500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8477 25.94 - 51.87: 504 51.87 - 77.81: 43 77.81 - 103.75: 10 103.75 - 129.68: 16 Dihedral angle restraints: 9050 sinusoidal: 3767 harmonic: 5283 Sorted by residual: dihedral pdb=" C3' PCG B 802 " pdb=" O3' PCG B 802 " pdb=" PA PCG B 802 " pdb=" O2A PCG B 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.41 129.68 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG C 802 " pdb=" O3' PCG C 802 " pdb=" PA PCG C 802 " pdb=" O2A PCG C 802 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3' PCG D 901 " pdb=" O3' PCG D 901 " pdb=" PA PCG D 901 " pdb=" O2A PCG D 901 " ideal model delta sinusoidal sigma weight residual 279.09 149.46 129.63 1 3.00e+01 1.11e-03 1.75e+01 ... (remaining 9047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2329 0.356 - 0.712: 0 0.712 - 1.069: 0 1.069 - 1.425: 0 1.425 - 1.781: 4 Chirality restraints: 2333 Sorted by residual: chirality pdb=" C4' PCG C 802 " pdb=" C3' PCG C 802 " pdb=" C5' PCG C 802 " pdb=" O4' PCG C 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.93e+01 chirality pdb=" C4' PCG B 802 " pdb=" C3' PCG B 802 " pdb=" C5' PCG B 802 " pdb=" O4' PCG B 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.92e+01 chirality pdb=" C4' PCG A 802 " pdb=" C3' PCG A 802 " pdb=" C5' PCG A 802 " pdb=" O4' PCG A 802 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.91e+01 ... (remaining 2330 not shown) Planarity restraints: 2526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 272 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO D 273 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 502 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO D 503 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 503 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 503 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 411 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO D 412 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 412 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 412 " -0.033 5.00e-02 4.00e+02 ... (remaining 2523 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3552 2.79 - 3.31: 13288 3.31 - 3.84: 25514 3.84 - 4.37: 29262 4.37 - 4.90: 50796 Nonbonded interactions: 122412 Sorted by model distance: nonbonded pdb=" O THR C 360 " pdb=" OG1 THR C 364 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 551 " pdb=" OD1 ASN B 562 " model vdw 2.308 3.040 nonbonded pdb=" O THR B 360 " pdb=" OG1 THR B 364 " model vdw 2.313 3.040 nonbonded pdb=" O LEU C 195 " pdb=" NE1 TRP C 203 " model vdw 2.331 3.120 nonbonded pdb=" ND2 ASN B 317 " pdb=" OD1 ASP B 384 " model vdw 2.333 3.120 ... (remaining 122407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 611 or resid 801 through 802)) selection = (chain 'B' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 802)) selection = (chain 'C' and (resid 159 through 260 or resid 270 through 391 or resid 393 thro \ ugh 802)) } 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=0.30 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: 2.020 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.510 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 : 0.005 0.117 15105 Z= 0.260 Angle : 0.871 18.302 20514 Z= 0.420 Chirality : 0.088 1.781 2333 Planarity : 0.006 0.066 2523 Dihedral : 16.901 129.682 5656 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.93 % Allowed : 12.00 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.16), residues: 1781 helix: -1.60 (0.11), residues: 1152 sheet: -2.06 (0.59), residues: 55 loop : -1.36 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 603 TYR 0.016 0.002 TYR C 263 PHE 0.016 0.002 PHE B 426 TRP 0.020 0.002 TRP B 171 HIS 0.004 0.001 HIS A 473 Details of bonding type rmsd covalent geometry : bond 0.00540 (15102) covalent geometry : angle 0.87040 (20505) hydrogen bonds : bond 0.10848 ( 938) hydrogen bonds : angle 5.34039 ( 2724) link_NAG-ASN : bond 0.00148 ( 3) link_NAG-ASN : angle 1.92624 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.454 Fit side-chains REVERT: C 418 ASP cc_start: 0.8157 (m-30) cc_final: 0.7942 (m-30) REVERT: C 515 ILE cc_start: 0.8906 (mm) cc_final: 0.8671 (mm) REVERT: D 249 ASN cc_start: 0.7504 (t0) cc_final: 0.7070 (t0) outliers start: 15 outliers final: 5 residues processed: 223 average time/residue: 0.1352 time to fit residues: 42.3358 Evaluate side-chains 151 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 146 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 448 LYS Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain C residue 563 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 GLN A 296 ASN A 562 ASN A 610 ASN B 196 GLN B 229 GLN B 242 HIS B 276 ASN B 407 ASN C 241 GLN C 248 GLN C 317 ASN C 398 ASN C 471 ASN C 473 HIS C 554 ASN D 232 ASN D 340 HIS D 365 HIS D 367 ASN D 423 GLN D 426 ASN D 440 GLN D 531 GLN D 602 ASN D 630 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.112640 restraints weight = 26170.243| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.88 r_work: 0.2948 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15105 Z= 0.132 Angle : 0.504 8.032 20514 Z= 0.268 Chirality : 0.041 0.186 2333 Planarity : 0.004 0.055 2523 Dihedral : 12.992 146.390 2183 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.49 % Allowed : 14.61 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1781 helix: 0.46 (0.14), residues: 1126 sheet: -1.61 (0.60), residues: 55 loop : -0.79 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 274 TYR 0.013 0.001 TYR C 508 PHE 0.016 0.001 PHE A 426 TRP 0.015 0.001 TRP A 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00296 (15102) covalent geometry : angle 0.50241 (20505) hydrogen bonds : bond 0.04131 ( 938) hydrogen bonds : angle 4.35113 ( 2724) link_NAG-ASN : bond 0.00097 ( 3) link_NAG-ASN : angle 1.82149 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.435 Fit side-chains REVERT: A 481 ARG cc_start: 0.7395 (ptt180) cc_final: 0.7081 (ptt180) REVERT: A 501 THR cc_start: 0.7656 (m) cc_final: 0.7336 (p) REVERT: A 546 TYR cc_start: 0.8371 (p90) cc_final: 0.8026 (p90) REVERT: B 162 ASP cc_start: 0.8016 (p0) cc_final: 0.7806 (p0) REVERT: B 274 ARG cc_start: 0.7889 (mtp85) cc_final: 0.7687 (mtp85) REVERT: B 296 ASN cc_start: 0.6784 (p0) cc_final: 0.6319 (p0) REVERT: B 402 MET cc_start: 0.8625 (ttp) cc_final: 0.8378 (ttm) REVERT: B 497 LYS cc_start: 0.8093 (mttp) cc_final: 0.7668 (mttp) REVERT: B 546 TYR cc_start: 0.8486 (p90) cc_final: 0.8088 (p90) REVERT: C 418 ASP cc_start: 0.8633 (m-30) cc_final: 0.8347 (m-30) REVERT: D 249 ASN cc_start: 0.7488 (t0) cc_final: 0.6725 (t0) REVERT: D 252 TYR cc_start: 0.6203 (t80) cc_final: 0.5267 (m-80) REVERT: D 344 ILE cc_start: 0.8177 (tp) cc_final: 0.7973 (pt) REVERT: D 443 ASP cc_start: 0.8493 (t70) cc_final: 0.8238 (t70) REVERT: D 536 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7456 (ptp) outliers start: 24 outliers final: 15 residues processed: 183 average time/residue: 0.1058 time to fit residues: 29.7721 Evaluate side-chains 161 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 563 ARG Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 31 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 79 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.0470 chunk 53 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN C 554 ASN D 230 ASN D 440 GLN D 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.155600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.120650 restraints weight = 25750.342| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 3.87 r_work: 0.2799 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15105 Z= 0.116 Angle : 0.475 8.394 20514 Z= 0.251 Chirality : 0.040 0.178 2333 Planarity : 0.004 0.055 2523 Dihedral : 12.672 151.399 2175 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.62 % Allowed : 15.29 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1781 helix: 1.33 (0.15), residues: 1132 sheet: -0.85 (0.60), residues: 59 loop : -0.43 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 274 TYR 0.011 0.001 TYR C 263 PHE 0.013 0.001 PHE A 192 TRP 0.013 0.001 TRP A 445 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00260 (15102) covalent geometry : angle 0.47400 (20505) hydrogen bonds : bond 0.03853 ( 938) hydrogen bonds : angle 4.07305 ( 2724) link_NAG-ASN : bond 0.00069 ( 3) link_NAG-ASN : angle 1.83510 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.479 Fit side-chains REVERT: A 231 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7027 (tp) REVERT: A 481 ARG cc_start: 0.7373 (ptt180) cc_final: 0.7050 (ptt180) REVERT: A 501 THR cc_start: 0.7518 (m) cc_final: 0.7286 (p) REVERT: A 543 ASP cc_start: 0.7646 (t70) cc_final: 0.7385 (t0) REVERT: A 546 TYR cc_start: 0.8281 (p90) cc_final: 0.7979 (p90) REVERT: B 162 ASP cc_start: 0.7933 (p0) cc_final: 0.7578 (p0) REVERT: B 296 ASN cc_start: 0.6790 (p0) cc_final: 0.6252 (p0) REVERT: B 402 MET cc_start: 0.8662 (ttp) cc_final: 0.8453 (ttm) REVERT: B 497 LYS cc_start: 0.8074 (mttp) cc_final: 0.7627 (mttp) REVERT: B 546 TYR cc_start: 0.8477 (p90) cc_final: 0.8062 (p90) REVERT: C 292 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7637 (tt0) REVERT: C 418 ASP cc_start: 0.8619 (m-30) cc_final: 0.8363 (m-30) REVERT: D 213 TYR cc_start: 0.7426 (t80) cc_final: 0.7178 (t80) REVERT: D 249 ASN cc_start: 0.7297 (t0) cc_final: 0.6622 (t0) REVERT: D 252 TYR cc_start: 0.6253 (t80) cc_final: 0.5310 (m-80) REVERT: D 344 ILE cc_start: 0.8266 (tp) cc_final: 0.8026 (pt) REVERT: D 424 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8465 (tp) REVERT: D 443 ASP cc_start: 0.8508 (t70) cc_final: 0.8276 (t70) REVERT: D 536 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7405 (ptp) REVERT: D 559 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7505 (ptmm) outliers start: 26 outliers final: 15 residues processed: 177 average time/residue: 0.0982 time to fit residues: 26.6514 Evaluate side-chains 165 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 167 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 156 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.0270 chunk 132 optimal weight: 8.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 ASN B 299 ASN B 473 HIS D 440 GLN D 630 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.156961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123818 restraints weight = 32150.842| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.39 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15105 Z= 0.103 Angle : 0.458 8.276 20514 Z= 0.241 Chirality : 0.039 0.175 2333 Planarity : 0.003 0.053 2523 Dihedral : 12.474 152.273 2171 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.37 % Allowed : 16.28 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1781 helix: 1.80 (0.15), residues: 1132 sheet: -0.80 (0.58), residues: 61 loop : -0.15 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 274 TYR 0.010 0.001 TYR C 357 PHE 0.011 0.001 PHE D 270 TRP 0.012 0.001 TRP A 445 HIS 0.003 0.001 HIS B 473 Details of bonding type rmsd covalent geometry : bond 0.00227 (15102) covalent geometry : angle 0.45644 (20505) hydrogen bonds : bond 0.03645 ( 938) hydrogen bonds : angle 3.87580 ( 2724) link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 1.76430 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.520 Fit side-chains REVERT: A 231 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7100 (tp) REVERT: A 543 ASP cc_start: 0.7474 (t70) cc_final: 0.7175 (t0) REVERT: A 546 TYR cc_start: 0.8094 (p90) cc_final: 0.7894 (p90) REVERT: B 245 THR cc_start: 0.7749 (t) cc_final: 0.7421 (p) REVERT: B 410 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7190 (ttp80) REVERT: B 546 TYR cc_start: 0.8190 (p90) cc_final: 0.7790 (p90) REVERT: C 418 ASP cc_start: 0.8100 (m-30) cc_final: 0.7877 (m-30) REVERT: D 249 ASN cc_start: 0.7234 (t0) cc_final: 0.6599 (t0) REVERT: D 252 TYR cc_start: 0.6275 (t80) cc_final: 0.5498 (m-80) REVERT: D 424 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7744 (tp) REVERT: D 536 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.7211 (ptp) REVERT: D 559 LYS cc_start: 0.8158 (ptmt) cc_final: 0.7534 (ptmm) outliers start: 22 outliers final: 12 residues processed: 184 average time/residue: 0.1024 time to fit residues: 29.1198 Evaluate side-chains 161 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 70 optimal weight: 1.9990 chunk 150 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 120 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 HIS D 440 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.152613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120312 restraints weight = 26071.176| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.50 r_work: 0.2751 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 15105 Z= 0.176 Angle : 0.528 11.814 20514 Z= 0.275 Chirality : 0.042 0.209 2333 Planarity : 0.004 0.052 2523 Dihedral : 12.493 153.538 2171 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.86 % Allowed : 16.03 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1781 helix: 1.68 (0.15), residues: 1134 sheet: -0.39 (0.59), residues: 59 loop : -0.13 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 274 TYR 0.015 0.001 TYR C 354 PHE 0.020 0.001 PHE C 192 TRP 0.013 0.001 TRP A 445 HIS 0.005 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00430 (15102) covalent geometry : angle 0.52659 (20505) hydrogen bonds : bond 0.04202 ( 938) hydrogen bonds : angle 4.03761 ( 2724) link_NAG-ASN : bond 0.00089 ( 3) link_NAG-ASN : angle 1.73761 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.512 Fit side-chains REVERT: A 184 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7326 (m-80) REVERT: A 231 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7107 (tp) REVERT: A 543 ASP cc_start: 0.7782 (t70) cc_final: 0.7479 (t0) REVERT: A 546 TYR cc_start: 0.8299 (p90) cc_final: 0.8072 (p90) REVERT: B 296 ASN cc_start: 0.6843 (p0) cc_final: 0.6264 (p0) REVERT: B 455 GLU cc_start: 0.7561 (tp30) cc_final: 0.7285 (tp30) REVERT: B 471 ASN cc_start: 0.8728 (t0) cc_final: 0.8385 (t0) REVERT: B 546 TYR cc_start: 0.8466 (p90) cc_final: 0.8003 (p90) REVERT: C 418 ASP cc_start: 0.8702 (m-30) cc_final: 0.8454 (m-30) REVERT: C 515 ILE cc_start: 0.8404 (mm) cc_final: 0.8131 (mm) REVERT: D 249 ASN cc_start: 0.7388 (t0) cc_final: 0.6772 (t0) REVERT: D 252 TYR cc_start: 0.6393 (t80) cc_final: 0.5392 (m-80) REVERT: D 424 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8556 (tp) REVERT: D 536 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7533 (ptp) REVERT: D 559 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7486 (ptmm) outliers start: 30 outliers final: 20 residues processed: 185 average time/residue: 0.0991 time to fit residues: 28.2108 Evaluate side-chains 181 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 36 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 138 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.155658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125214 restraints weight = 28682.048| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 3.49 r_work: 0.2783 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15105 Z= 0.112 Angle : 0.464 9.394 20514 Z= 0.245 Chirality : 0.040 0.175 2333 Planarity : 0.003 0.051 2523 Dihedral : 12.362 153.619 2171 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.68 % Allowed : 16.53 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1781 helix: 1.93 (0.15), residues: 1132 sheet: -0.32 (0.60), residues: 61 loop : 0.02 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 274 TYR 0.010 0.001 TYR C 357 PHE 0.012 0.001 PHE C 301 TRP 0.013 0.001 TRP B 171 HIS 0.003 0.001 HIS D 630 Details of bonding type rmsd covalent geometry : bond 0.00253 (15102) covalent geometry : angle 0.46297 (20505) hydrogen bonds : bond 0.03719 ( 938) hydrogen bonds : angle 3.84659 ( 2724) link_NAG-ASN : bond 0.00056 ( 3) link_NAG-ASN : angle 1.74414 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.571 Fit side-chains REVERT: A 184 TYR cc_start: 0.7512 (OUTLIER) cc_final: 0.7287 (m-80) REVERT: A 231 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7067 (tp) REVERT: A 543 ASP cc_start: 0.7774 (t70) cc_final: 0.7480 (t0) REVERT: A 546 TYR cc_start: 0.8233 (p90) cc_final: 0.8005 (p90) REVERT: B 497 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7951 (mmtm) REVERT: B 546 TYR cc_start: 0.8416 (p90) cc_final: 0.7893 (p90) REVERT: C 515 ILE cc_start: 0.8368 (mm) cc_final: 0.8094 (mm) REVERT: D 249 ASN cc_start: 0.7244 (t0) cc_final: 0.6560 (t0) REVERT: D 252 TYR cc_start: 0.6337 (t80) cc_final: 0.5298 (m-80) REVERT: D 268 MET cc_start: 0.7895 (tpp) cc_final: 0.7496 (ttm) REVERT: D 424 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8399 (tp) REVERT: D 523 ASP cc_start: 0.7347 (t0) cc_final: 0.6969 (p0) REVERT: D 536 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7518 (ptp) REVERT: D 559 LYS cc_start: 0.8262 (ptmt) cc_final: 0.7491 (ptmm) outliers start: 27 outliers final: 15 residues processed: 182 average time/residue: 0.1055 time to fit residues: 29.4814 Evaluate side-chains 173 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 93 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 123 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.154886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120897 restraints weight = 27228.261| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.98 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15105 Z= 0.124 Angle : 0.472 8.389 20514 Z= 0.249 Chirality : 0.040 0.182 2333 Planarity : 0.003 0.050 2523 Dihedral : 12.318 153.258 2171 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.62 % Allowed : 16.90 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1781 helix: 1.99 (0.15), residues: 1132 sheet: -0.22 (0.61), residues: 61 loop : 0.07 (0.28), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.012 0.001 TYR C 354 PHE 0.015 0.001 PHE A 192 TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00289 (15102) covalent geometry : angle 0.47058 (20505) hydrogen bonds : bond 0.03825 ( 938) hydrogen bonds : angle 3.82191 ( 2724) link_NAG-ASN : bond 0.00064 ( 3) link_NAG-ASN : angle 1.69874 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.563 Fit side-chains REVERT: A 231 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7211 (tp) REVERT: A 543 ASP cc_start: 0.7631 (t70) cc_final: 0.7294 (t0) REVERT: B 546 TYR cc_start: 0.8130 (p90) cc_final: 0.7745 (p90) REVERT: C 418 ASP cc_start: 0.8194 (m-30) cc_final: 0.7979 (m-30) REVERT: C 515 ILE cc_start: 0.8820 (mm) cc_final: 0.8556 (mm) REVERT: D 249 ASN cc_start: 0.7289 (t0) cc_final: 0.6834 (t0) REVERT: D 252 TYR cc_start: 0.6366 (t80) cc_final: 0.5589 (m-80) REVERT: D 424 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7959 (tp) REVERT: D 536 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7413 (ptp) REVERT: D 559 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7636 (ptmm) outliers start: 26 outliers final: 17 residues processed: 178 average time/residue: 0.1000 time to fit residues: 27.5132 Evaluate side-chains 171 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 52 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 131 optimal weight: 0.0970 chunk 151 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 345 HIS D 440 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.156330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.119767 restraints weight = 24586.561| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.85 r_work: 0.2798 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15105 Z= 0.108 Angle : 0.457 9.502 20514 Z= 0.241 Chirality : 0.040 0.180 2333 Planarity : 0.003 0.051 2523 Dihedral : 12.253 153.795 2171 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.43 % Allowed : 17.28 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.21), residues: 1781 helix: 2.11 (0.15), residues: 1133 sheet: -0.01 (0.64), residues: 61 loop : 0.13 (0.28), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.010 0.001 TYR C 357 PHE 0.016 0.001 PHE A 180 TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00241 (15102) covalent geometry : angle 0.45572 (20505) hydrogen bonds : bond 0.03673 ( 938) hydrogen bonds : angle 3.74321 ( 2724) link_NAG-ASN : bond 0.00062 ( 3) link_NAG-ASN : angle 1.67211 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.455 Fit side-chains REVERT: A 184 TYR cc_start: 0.7632 (m-80) cc_final: 0.7224 (m-80) REVERT: A 231 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7047 (tp) REVERT: A 543 ASP cc_start: 0.7806 (t70) cc_final: 0.7524 (t0) REVERT: B 546 TYR cc_start: 0.8410 (p90) cc_final: 0.7843 (p90) REVERT: C 418 ASP cc_start: 0.8668 (m-30) cc_final: 0.8413 (m-30) REVERT: C 515 ILE cc_start: 0.8359 (mm) cc_final: 0.8093 (mm) REVERT: D 249 ASN cc_start: 0.7203 (t0) cc_final: 0.6532 (t0) REVERT: D 252 TYR cc_start: 0.6344 (t80) cc_final: 0.5258 (m-80) REVERT: D 424 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 466 MET cc_start: 0.8969 (mtm) cc_final: 0.8764 (mtm) REVERT: D 523 ASP cc_start: 0.7362 (p0) cc_final: 0.6661 (t0) REVERT: D 536 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7458 (ptp) REVERT: D 559 LYS cc_start: 0.8267 (ptmt) cc_final: 0.7524 (ptmm) outliers start: 23 outliers final: 17 residues processed: 178 average time/residue: 0.0907 time to fit residues: 25.6476 Evaluate side-chains 171 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 476 THR Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 164 optimal weight: 6.9990 chunk 166 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 144 optimal weight: 0.0870 chunk 146 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 134 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123783 restraints weight = 35778.972| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.62 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15105 Z= 0.106 Angle : 0.453 9.545 20514 Z= 0.240 Chirality : 0.039 0.173 2333 Planarity : 0.003 0.051 2523 Dihedral : 12.212 153.752 2171 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.55 % Allowed : 17.28 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.21), residues: 1781 helix: 2.18 (0.15), residues: 1139 sheet: 0.04 (0.64), residues: 61 loop : 0.13 (0.29), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.010 0.001 TYR D 399 PHE 0.012 0.001 PHE A 192 TRP 0.012 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00238 (15102) covalent geometry : angle 0.45230 (20505) hydrogen bonds : bond 0.03632 ( 938) hydrogen bonds : angle 3.69846 ( 2724) link_NAG-ASN : bond 0.00063 ( 3) link_NAG-ASN : angle 1.62939 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.447 Fit side-chains REVERT: A 184 TYR cc_start: 0.7173 (m-80) cc_final: 0.6906 (m-80) REVERT: A 231 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7228 (tp) REVERT: A 543 ASP cc_start: 0.7659 (t70) cc_final: 0.7309 (t0) REVERT: B 232 MET cc_start: 0.7701 (ttm) cc_final: 0.7376 (ttm) REVERT: B 458 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7882 (mtpt) REVERT: B 546 TYR cc_start: 0.8105 (p90) cc_final: 0.7656 (p90) REVERT: C 418 ASP cc_start: 0.8124 (m-30) cc_final: 0.7917 (m-30) REVERT: C 515 ILE cc_start: 0.8792 (mm) cc_final: 0.8534 (mm) REVERT: D 249 ASN cc_start: 0.7216 (t0) cc_final: 0.6824 (t0) REVERT: D 252 TYR cc_start: 0.6465 (t80) cc_final: 0.5598 (m-80) REVERT: D 424 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7903 (tp) REVERT: D 523 ASP cc_start: 0.7190 (p0) cc_final: 0.6736 (t0) REVERT: D 536 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.7416 (ptp) REVERT: D 559 LYS cc_start: 0.8257 (ptmt) cc_final: 0.7769 (ptmm) REVERT: D 560 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7908 (mt-10) outliers start: 25 outliers final: 15 residues processed: 181 average time/residue: 0.0947 time to fit residues: 26.9369 Evaluate side-chains 174 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 chunk 43 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 440 GLN D 630 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.157960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.126111 restraints weight = 30760.697| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.84 r_work: 0.2809 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15105 Z= 0.098 Angle : 0.449 9.476 20514 Z= 0.237 Chirality : 0.039 0.169 2333 Planarity : 0.003 0.052 2523 Dihedral : 12.164 154.028 2171 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.12 % Allowed : 17.65 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.21), residues: 1781 helix: 2.26 (0.15), residues: 1140 sheet: 0.06 (0.67), residues: 58 loop : 0.14 (0.29), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.010 0.001 TYR C 357 PHE 0.011 0.001 PHE A 180 TRP 0.012 0.001 TRP B 171 HIS 0.002 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00214 (15102) covalent geometry : angle 0.44756 (20505) hydrogen bonds : bond 0.03524 ( 938) hydrogen bonds : angle 3.65812 ( 2724) link_NAG-ASN : bond 0.00078 ( 3) link_NAG-ASN : angle 1.58672 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.412 Fit side-chains REVERT: A 184 TYR cc_start: 0.7722 (m-80) cc_final: 0.7307 (m-80) REVERT: A 231 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7074 (tp) REVERT: A 543 ASP cc_start: 0.7799 (t70) cc_final: 0.7522 (t0) REVERT: A 546 TYR cc_start: 0.8467 (p90) cc_final: 0.8232 (p90) REVERT: B 232 MET cc_start: 0.7781 (ttm) cc_final: 0.7534 (ttm) REVERT: B 458 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7646 (mtpt) REVERT: B 546 TYR cc_start: 0.8388 (p90) cc_final: 0.7852 (p90) REVERT: C 193 ASP cc_start: 0.7813 (t70) cc_final: 0.7229 (t0) REVERT: C 418 ASP cc_start: 0.8642 (m-30) cc_final: 0.8381 (m-30) REVERT: C 515 ILE cc_start: 0.8375 (mm) cc_final: 0.8101 (mm) REVERT: D 252 TYR cc_start: 0.6342 (t80) cc_final: 0.5301 (m-80) REVERT: D 424 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8358 (tp) REVERT: D 523 ASP cc_start: 0.7344 (p0) cc_final: 0.6605 (t0) REVERT: D 536 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7361 (ptp) REVERT: D 559 LYS cc_start: 0.8320 (ptmt) cc_final: 0.7619 (ptmm) REVERT: D 560 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8168 (mt-10) outliers start: 18 outliers final: 12 residues processed: 179 average time/residue: 0.0879 time to fit residues: 24.7571 Evaluate side-chains 175 residues out of total 1605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 255 SER Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 578 CYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 536 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 153 optimal weight: 0.0070 chunk 80 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 154 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 249 ASN D 440 GLN D 630 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.157454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122199 restraints weight = 23635.493| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 3.52 r_work: 0.2843 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15105 Z= 0.106 Angle : 0.458 9.619 20514 Z= 0.241 Chirality : 0.039 0.168 2333 Planarity : 0.003 0.051 2523 Dihedral : 12.159 153.943 2171 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.18 % Allowed : 17.65 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.21), residues: 1781 helix: 2.27 (0.15), residues: 1139 sheet: 0.13 (0.67), residues: 58 loop : 0.17 (0.29), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 274 TYR 0.010 0.001 TYR D 399 PHE 0.014 0.001 PHE A 192 TRP 0.011 0.001 TRP B 171 HIS 0.003 0.001 HIS D 365 Details of bonding type rmsd covalent geometry : bond 0.00239 (15102) covalent geometry : angle 0.45672 (20505) hydrogen bonds : bond 0.03563 ( 938) hydrogen bonds : angle 3.65841 ( 2724) link_NAG-ASN : bond 0.00047 ( 3) link_NAG-ASN : angle 1.57017 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.01 seconds wall clock time: 55 minutes 1.27 seconds (3301.27 seconds total)