Starting phenix.real_space_refine on Fri Jun 13 00:52:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625.map" model { file = "/net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evb_28625/06_2025/8evb_28625_neut.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 65 5.16 5 C 9427 2.51 5 N 2354 2.21 5 O 2606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 137 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14456 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 444, 3618 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 13, 'TRANS': 430} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 444, 3618 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 13, 'TRANS': 430} Chain breaks: 1 bond proxies already assigned to first conformer: 3686 Chain: "B" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3532 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 13, 'TRANS': 418} Chain breaks: 3 Chain: "C" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3576 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 14, 'TRANS': 423} Chain breaks: 1 Chain: "D" Number of atoms: 3585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3585 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 13, 'TRANS': 423} Chain breaks: 1 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=0.60 ... (20 atoms not shown) pdb=" CZ BPHE A 392 " occ=0.40 Time building chain proxies: 10.66, per 1000 atoms: 0.74 Number of scatterers: 14456 At special positions: 0 Unit cell: (103.75, 110.39, 125.33, 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 65 16.00 P 4 15.00 O 2606 8.00 N 2354 7.00 C 9427 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: 3.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3322 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 12 sheets defined 64.8% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 165 through 192 Proline residue: A 178 - end of helix removed outlier: 5.431A pdb=" N ILE A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N CYS A 188 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.970A pdb=" N GLN A 196 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 222 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.916A pdb=" N LYS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 279 removed outlier: 4.164A pdb=" N ASN A 276 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 295 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 406 Processing helix chain 'A' and resid 409 through 428 removed outlier: 3.559A pdb=" N PHE A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) 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 473 removed outlier: 3.551A pdb=" N HIS A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) 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 553 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 592 through 609 Processing helix chain 'B' and resid 165 through 193 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 199 through 223 removed outlier: 4.336A pdb=" N TRP B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.177A 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 343 through 346 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 374 through 404 removed outlier: 3.577A pdb=" N VAL B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 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 477 Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 591 through 610 Processing helix chain 'C' and resid 165 through 193 removed outlier: 3.896A pdb=" N LEU C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.818A pdb=" N CYS C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASP C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 222 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 247 through 255 Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 281 through 295 removed outlier: 3.706A pdb=" N PHE C 285 " --> pdb=" O PHE C 281 " (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 Processing helix chain 'C' and resid 407 through 428 Processing helix chain 'C' and resid 430 through 447 Processing helix chain 'C' and resid 453 through 458 Processing helix chain 'C' and resid 461 through 478 removed outlier: 4.595A pdb=" N ASN C 471 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N HIS C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.818A pdb=" N LEU C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 592 through 607 Processing helix chain 'D' and resid 215 through 242 removed outlier: 4.069A pdb=" N ASN D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Proline residue: D 237 - end of helix Processing helix chain 'D' and resid 249 through 270 Processing helix chain 'D' and resid 271 through 275 removed outlier: 4.046A pdb=" N LEU D 275 " --> pdb=" O GLN D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 297 removed outlier: 3.738A pdb=" N LEU D 290 " --> pdb=" O ASP D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 307 Processing helix chain 'D' and resid 310 through 315 Processing helix chain 'D' and resid 330 through 345 Processing helix chain 'D' and resid 347 through 379 removed outlier: 4.372A pdb=" N TYR D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 416 through 449 removed outlier: 3.756A pdb=" N GLY D 439 " --> pdb=" O SER D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 469 Processing helix chain 'D' and resid 472 through 491 Processing helix chain 'D' and resid 495 through 500 Processing helix chain 'D' and resid 503 through 520 removed outlier: 3.507A pdb=" N SER D 517 " --> pdb=" O ASP D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 621 through 629 Processing helix chain 'D' and resid 631 through 645 removed outlier: 3.504A pdb=" N GLU D 635 " --> pdb=" O TYR D 631 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 499 through 503 removed outlier: 3.530A pdb=" N ARG A 499 " --> pdb=" O CYS A 578 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 574 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 521 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.777A pdb=" N CYS A 510 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG A 569 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA A 528 " --> pdb=" O ARG A 569 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 527 " --> pdb=" O VAL A 540 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL A 540 " --> pdb=" O LEU A 527 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL A 529 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 227 through 228 Processing sheet with id=AA4, first strand: chain 'B' and resid 499 through 503 removed outlier: 4.153A pdb=" N ASP B 575 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 523 " --> pdb=" O ASP B 575 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 508 through 510 removed outlier: 6.849A pdb=" N ILE B 568 " --> pdb=" O ILE B 509 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 569 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 528 " --> pdb=" O ARG B 569 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 527 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 514 through 515 removed outlier: 3.957A pdb=" N ASP B 514 " --> pdb=" O ARG B 564 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 564 " --> pdb=" O ASP B 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 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 501 through 503 Processing sheet with id=AA9, first strand: chain 'C' and resid 508 through 510 removed outlier: 7.166A pdb=" N ILE C 568 " --> pdb=" O ILE C 509 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 539 " --> pdb=" O VAL C 529 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 278 through 279 Processing sheet with id=AB2, first strand: chain 'D' and resid 541 through 545 removed outlier: 3.810A pdb=" N LYS D 541 " --> pdb=" O THR D 618 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 550 through 552 removed outlier: 7.380A pdb=" N VAL D 608 " --> pdb=" O VAL D 551 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 569 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 584 " --> pdb=" O VAL D 569 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N VAL D 582 " --> pdb=" O VAL D 571 " (cutoff:3.500A) 890 hydrogen bonds defined for protein. 2629 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: 4.12 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2294 1.32 - 1.44: 4170 1.44 - 1.57: 8234 1.57 - 1.70: 0 1.70 - 1.83: 104 Bond restraints: 14802 Sorted by residual: 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 3.40e+01 bond pdb=" O5' PCG A 802 " pdb=" PA PCG A 802 " ideal model delta sigma weight residual 1.606 1.490 0.116 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 3.38e+01 bond pdb=" O5' PCG C 802 " pdb=" PA PCG C 802 " ideal model delta sigma weight residual 1.606 1.491 0.115 2.00e-02 2.50e+03 3.33e+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 2.71e+01 ... (remaining 14797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 19669 3.66 - 7.33: 351 7.33 - 10.99: 52 10.99 - 14.66: 4 14.66 - 18.32: 12 Bond angle restraints: 20088 Sorted by residual: angle pdb=" C GLN D 272 " pdb=" N PRO D 273 " pdb=" CA PRO D 273 " ideal model delta sigma weight residual 121.65 114.66 6.99 1.01e+00 9.80e-01 4.79e+01 angle pdb=" C3' PCG D 901 " pdb=" C4' PCG D 901 " pdb=" C5' PCG D 901 " ideal model delta sigma weight residual 109.85 128.17 -18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C3' PCG C 802 " pdb=" C4' PCG C 802 " pdb=" C5' PCG C 802 " ideal model delta sigma weight residual 109.85 128.11 -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 B 802 " pdb=" C4' PCG B 802 " pdb=" C5' PCG B 802 " ideal model delta sigma weight residual 109.85 128.09 -18.24 3.00e+00 1.11e-01 3.70e+01 ... (remaining 20083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.94: 8257 25.94 - 51.88: 548 51.88 - 77.82: 36 77.82 - 103.75: 2 103.75 - 129.69: 16 Dihedral angle restraints: 8859 sinusoidal: 3693 harmonic: 5166 Sorted by residual: dihedral pdb=" CA VAL C 480 " pdb=" C VAL C 480 " pdb=" N ARG C 481 " pdb=" CA ARG C 481 " ideal model delta harmonic sigma weight residual 180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA GLY B 544 " pdb=" C GLY B 544 " pdb=" N SER B 545 " pdb=" CA SER B 545 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA ALA A 469 " pdb=" C ALA A 469 " pdb=" N ILE A 470 " pdb=" CA ILE A 470 " ideal model delta harmonic sigma weight residual 180.00 156.66 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 8856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.356: 2279 0.356 - 0.713: 0 0.713 - 1.069: 0 1.069 - 1.425: 0 1.425 - 1.782: 4 Chirality restraints: 2283 Sorted by residual: 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 7.94e+01 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 D 901 " pdb=" C3' PCG D 901 " pdb=" C5' PCG D 901 " pdb=" O4' PCG D 901 " both_signs ideal model delta sigma weight residual False -2.50 -0.72 -1.78 2.00e-01 2.50e+01 7.92e+01 ... (remaining 2280 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 406 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ILE D 406 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE D 406 " 0.023 2.00e-02 2.50e+03 pdb=" N THR D 407 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 609 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" CG ASP A 609 " -0.057 2.00e-02 2.50e+03 pdb=" OD1 ASP A 609 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP A 609 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 182 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C ASN C 182 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN C 182 " -0.021 2.00e-02 2.50e+03 pdb=" N TRP C 183 " -0.019 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 287 2.67 - 3.23: 12867 3.23 - 3.79: 23742 3.79 - 4.34: 29107 4.34 - 4.90: 47892 Nonbonded interactions: 113895 Sorted by model distance: nonbonded pdb=" O LEU C 278 " pdb=" CD1 LEU C 278 " model vdw 2.116 3.460 nonbonded pdb=" OD1 ASN B 299 " pdb=" CE MET B 402 " model vdw 2.199 3.460 nonbonded pdb=" O ASN C 182 " pdb=" CB LEU C 186 " model vdw 2.261 2.752 nonbonded pdb=" O GLY D 591 " pdb=" O2A PCG D 901 " model vdw 2.304 3.040 nonbonded pdb=" OG SER C 558 " pdb=" O ILE C 605 " model vdw 2.308 3.040 ... (remaining 113890 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 257 or resid 270 through 391 or resid 393 thro \ ugh 483 or resid 489 through 552 or resid 557 through 607 or resid 801 through 8 \ 02)) selection = (chain 'B' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ ugh 607 or resid 801 through 802)) selection = (chain 'C' and (resid 159 through 257 or resid 270 through 391 or resid 393 thro \ ugh 483 or resid 489 through 552 or resid 557 through 607 or resid 801 through 8 \ 02)) } 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 212.850 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: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.040 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.009 0.117 14805 Z= 0.407 Angle : 1.280 18.320 20097 Z= 0.659 Chirality : 0.101 1.782 2283 Planarity : 0.010 0.076 2465 Dihedral : 17.036 129.692 5537 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.63 % Allowed : 12.25 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.13), residues: 1734 helix: -3.41 (0.08), residues: 1111 sheet: -2.06 (0.55), residues: 53 loop : -3.02 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 221 HIS 0.005 0.002 HIS C 242 PHE 0.028 0.003 PHE A 301 TYR 0.037 0.003 TYR B 199 ARG 0.014 0.001 ARG D 324 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 3) link_NAG-ASN : angle 3.88540 ( 9) hydrogen bonds : bond 0.11860 ( 890) hydrogen bonds : angle 7.05023 ( 2629) covalent geometry : bond 0.00876 (14802) covalent geometry : angle 1.27763 (20088) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 279 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7890 (tp-100) cc_final: 0.7613 (tp-100) REVERT: A 467 GLU cc_start: 0.7997 (tp30) cc_final: 0.7754 (tp30) REVERT: B 229 GLN cc_start: 0.7969 (tt0) cc_final: 0.7162 (tt0) REVERT: B 417 ILE cc_start: 0.9083 (mt) cc_final: 0.8075 (mt) REVERT: B 422 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8709 (tm-30) REVERT: B 607 MET cc_start: 0.6931 (mmp) cc_final: 0.6605 (ttm) REVERT: C 188 CYS cc_start: 0.8204 (t) cc_final: 0.7685 (t) REVERT: C 228 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7270 (tp30) REVERT: C 229 GLN cc_start: 0.7560 (mt0) cc_final: 0.7235 (pt0) REVERT: C 276 ASN cc_start: 0.6253 (m-40) cc_final: 0.6035 (m-40) REVERT: C 299 ASN cc_start: 0.7670 (m110) cc_final: 0.7030 (p0) REVERT: C 422 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8796 (tm-30) REVERT: C 573 TYR cc_start: 0.8805 (m-80) cc_final: 0.8362 (m-80) REVERT: C 585 MET cc_start: 0.8930 (mmp) cc_final: 0.8540 (mmp) outliers start: 9 outliers final: 5 residues processed: 284 average time/residue: 0.2511 time to fit residues: 106.4218 Evaluate side-chains 192 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain D residue 272 GLN Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 537 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS A 407 ASN A 523 ASN ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 317 ASN C 241 GLN C 276 ASN C 317 ASN C 345 HIS D 367 ASN D 426 ASN D 611 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.134397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.103077 restraints weight = 53282.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107045 restraints weight = 21591.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109621 restraints weight = 12247.855| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14805 Z= 0.141 Angle : 0.650 12.994 20097 Z= 0.332 Chirality : 0.041 0.211 2283 Planarity : 0.005 0.053 2465 Dihedral : 13.648 165.744 2135 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.22 % Allowed : 17.51 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.17), residues: 1734 helix: -0.82 (0.14), residues: 1115 sheet: -1.48 (0.60), residues: 56 loop : -2.47 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 221 HIS 0.010 0.001 HIS C 242 PHE 0.045 0.001 PHE B 413 TYR 0.017 0.001 TYR C 546 ARG 0.007 0.001 ARG B 283 Details of bonding type rmsd link_NAG-ASN : bond 0.00152 ( 3) link_NAG-ASN : angle 2.78737 ( 9) hydrogen bonds : bond 0.04518 ( 890) hydrogen bonds : angle 5.02423 ( 2629) covalent geometry : bond 0.00297 (14802) covalent geometry : angle 0.64728 (20088) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 224 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 MET cc_start: 0.8451 (tpp) cc_final: 0.8213 (ttt) REVERT: A 352 TYR cc_start: 0.9056 (t80) cc_final: 0.8851 (t80) REVERT: A 424 MET cc_start: 0.7897 (mmp) cc_final: 0.7655 (mmp) REVERT: A 467 GLU cc_start: 0.8218 (tp30) cc_final: 0.8003 (tp30) REVERT: A 496 LEU cc_start: 0.8885 (tt) cc_final: 0.8635 (pp) REVERT: B 229 GLN cc_start: 0.7811 (tt0) cc_final: 0.7581 (tt0) REVERT: B 276 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7655 (t0) REVERT: B 279 LEU cc_start: 0.9026 (mp) cc_final: 0.8801 (mp) REVERT: B 305 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7528 (t0) REVERT: B 422 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8648 (tm-30) REVERT: C 175 ILE cc_start: 0.8811 (tp) cc_final: 0.8487 (tp) REVERT: C 188 CYS cc_start: 0.8227 (t) cc_final: 0.7765 (t) REVERT: C 299 ASN cc_start: 0.7759 (m110) cc_final: 0.7074 (p0) REVERT: C 410 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8156 (mtp85) REVERT: C 422 GLN cc_start: 0.9280 (tm-30) cc_final: 0.9076 (tm-30) REVERT: C 467 GLU cc_start: 0.8017 (tp30) cc_final: 0.7772 (tp30) REVERT: C 573 TYR cc_start: 0.8824 (m-80) cc_final: 0.8337 (m-80) REVERT: C 585 MET cc_start: 0.9156 (mmp) cc_final: 0.8804 (mmm) REVERT: D 268 MET cc_start: 0.8075 (tmm) cc_final: 0.7783 (tmm) REVERT: D 405 LEU cc_start: 0.9207 (tp) cc_final: 0.8842 (mp) REVERT: D 426 ASN cc_start: 0.8950 (OUTLIER) cc_final: 0.8429 (t0) outliers start: 34 outliers final: 16 residues processed: 247 average time/residue: 0.2522 time to fit residues: 94.8553 Evaluate side-chains 196 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 426 ASN Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 172 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 64 optimal weight: 0.0470 chunk 128 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 HIS D 272 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108947 restraints weight = 48119.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.112834 restraints weight = 20689.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.115400 restraints weight = 12113.084| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3632 r_free = 0.3632 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14805 Z= 0.136 Angle : 0.615 14.268 20097 Z= 0.309 Chirality : 0.041 0.203 2283 Planarity : 0.004 0.046 2465 Dihedral : 13.286 166.840 2125 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.54 % Allowed : 18.34 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1734 helix: 0.13 (0.15), residues: 1125 sheet: -1.35 (0.61), residues: 56 loop : -2.19 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 221 HIS 0.005 0.001 HIS C 242 PHE 0.030 0.001 PHE B 413 TYR 0.021 0.001 TYR B 184 ARG 0.005 0.000 ARG A 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 3) link_NAG-ASN : angle 2.55897 ( 9) hydrogen bonds : bond 0.04249 ( 890) hydrogen bonds : angle 4.67866 ( 2629) covalent geometry : bond 0.00297 (14802) covalent geometry : angle 0.61285 (20088) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 204 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 279 LEU cc_start: 0.9067 (mp) cc_final: 0.8806 (mp) REVERT: B 422 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8675 (tm-30) REVERT: B 434 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8497 (mm-30) REVERT: B 519 MET cc_start: 0.7038 (mtp) cc_final: 0.6737 (tpp) REVERT: B 607 MET cc_start: 0.7376 (mtt) cc_final: 0.7125 (mtp) REVERT: C 175 ILE cc_start: 0.8851 (tp) cc_final: 0.8528 (tp) REVERT: C 188 CYS cc_start: 0.8342 (t) cc_final: 0.7796 (t) REVERT: C 299 ASN cc_start: 0.7537 (m110) cc_final: 0.7004 (p0) REVERT: C 410 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8196 (mtp85) REVERT: C 422 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8969 (tm-30) REVERT: C 573 TYR cc_start: 0.8781 (m-80) cc_final: 0.8376 (m-80) REVERT: C 585 MET cc_start: 0.9086 (mmp) cc_final: 0.8652 (mmp) REVERT: D 419 GLU cc_start: 0.7650 (pt0) cc_final: 0.7422 (pt0) REVERT: D 539 ARG cc_start: 0.7940 (mmp-170) cc_final: 0.7503 (mmp-170) REVERT: D 630 HIS cc_start: 0.7157 (m-70) cc_final: 0.6936 (m-70) outliers start: 39 outliers final: 27 residues processed: 230 average time/residue: 0.2988 time to fit residues: 109.4141 Evaluate side-chains 208 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 119 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 56 optimal weight: 0.1980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.138243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.107020 restraints weight = 48879.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.110853 restraints weight = 21016.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.113361 restraints weight = 12319.684| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14805 Z= 0.159 Angle : 0.620 14.387 20097 Z= 0.310 Chirality : 0.042 0.232 2283 Planarity : 0.004 0.052 2465 Dihedral : 13.263 176.867 2123 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.68 % Allowed : 18.65 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1734 helix: 0.66 (0.15), residues: 1121 sheet: -1.13 (0.63), residues: 56 loop : -1.99 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 221 HIS 0.005 0.001 HIS A 315 PHE 0.047 0.001 PHE B 301 TYR 0.015 0.001 TYR D 454 ARG 0.005 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 3) link_NAG-ASN : angle 2.47358 ( 9) hydrogen bonds : bond 0.04242 ( 890) hydrogen bonds : angle 4.52706 ( 2629) covalent geometry : bond 0.00355 (14802) covalent geometry : angle 0.61776 (20088) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 190 time to evaluate : 1.666 Fit side-chains revert: symmetry clash REVERT: B 300 MET cc_start: 0.8138 (mmt) cc_final: 0.7806 (tpp) REVERT: B 305 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7767 (t0) REVERT: B 422 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 434 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 607 MET cc_start: 0.7363 (mtt) cc_final: 0.7122 (mtp) REVERT: C 175 ILE cc_start: 0.8912 (tp) cc_final: 0.8573 (tp) REVERT: C 188 CYS cc_start: 0.8415 (t) cc_final: 0.7866 (t) REVERT: C 299 ASN cc_start: 0.7524 (m110) cc_final: 0.7087 (p0) REVERT: C 410 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8220 (mtp85) REVERT: C 422 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8997 (tm-30) REVERT: C 573 TYR cc_start: 0.8781 (m-80) cc_final: 0.8350 (m-80) REVERT: C 585 MET cc_start: 0.9085 (mmp) cc_final: 0.8657 (mmp) REVERT: D 405 LEU cc_start: 0.9085 (tp) cc_final: 0.8740 (mp) REVERT: D 419 GLU cc_start: 0.7727 (pt0) cc_final: 0.7476 (pt0) REVERT: D 539 ARG cc_start: 0.7939 (mmp-170) cc_final: 0.7547 (mmp-170) REVERT: D 630 HIS cc_start: 0.7191 (m-70) cc_final: 0.6978 (m-70) outliers start: 57 outliers final: 37 residues processed: 233 average time/residue: 0.2046 time to fit residues: 76.1589 Evaluate side-chains 215 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 568 ILE Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 134 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 473 HIS D 476 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.140058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110095 restraints weight = 40699.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.113698 restraints weight = 18555.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.116058 restraints weight = 11261.810| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14805 Z= 0.119 Angle : 0.602 14.286 20097 Z= 0.296 Chirality : 0.041 0.300 2283 Planarity : 0.004 0.045 2465 Dihedral : 13.130 179.629 2123 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.54 % Allowed : 20.11 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.20), residues: 1734 helix: 0.98 (0.15), residues: 1120 sheet: -0.90 (0.65), residues: 56 loop : -1.92 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 221 HIS 0.004 0.001 HIS A 315 PHE 0.038 0.001 PHE B 301 TYR 0.014 0.001 TYR A 546 ARG 0.008 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 2.41503 ( 9) hydrogen bonds : bond 0.03971 ( 890) hydrogen bonds : angle 4.39538 ( 2629) covalent geometry : bond 0.00262 (14802) covalent geometry : angle 0.59956 (20088) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.9138 (t80) cc_final: 0.8897 (t80) REVERT: A 519 MET cc_start: 0.7640 (ttp) cc_final: 0.7363 (ttp) REVERT: B 276 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (t0) REVERT: B 300 MET cc_start: 0.8158 (mmt) cc_final: 0.7861 (tpp) REVERT: B 422 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8369 (tm-30) REVERT: B 434 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8217 (mm-30) REVERT: B 607 MET cc_start: 0.7243 (mtt) cc_final: 0.7007 (mtp) REVERT: C 175 ILE cc_start: 0.8818 (tp) cc_final: 0.8517 (tp) REVERT: C 188 CYS cc_start: 0.8321 (t) cc_final: 0.7755 (t) REVERT: C 299 ASN cc_start: 0.7378 (m110) cc_final: 0.7161 (p0) REVERT: C 410 ARG cc_start: 0.8654 (mtt90) cc_final: 0.8226 (mtp85) REVERT: C 422 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8972 (tm-30) REVERT: C 573 TYR cc_start: 0.8730 (m-80) cc_final: 0.8353 (m-80) REVERT: C 585 MET cc_start: 0.9046 (mmp) cc_final: 0.8710 (mmp) REVERT: D 405 LEU cc_start: 0.9025 (tp) cc_final: 0.8731 (mp) REVERT: D 419 GLU cc_start: 0.7627 (pt0) cc_final: 0.7370 (pt0) REVERT: D 539 ARG cc_start: 0.7912 (mmp-170) cc_final: 0.7538 (mmp-170) REVERT: D 630 HIS cc_start: 0.7160 (m-70) cc_final: 0.6954 (m-70) outliers start: 39 outliers final: 22 residues processed: 232 average time/residue: 0.2903 time to fit residues: 106.1826 Evaluate side-chains 207 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 171 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 150 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 GLN B 276 ASN B 305 ASN D 339 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.141112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.109550 restraints weight = 58523.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113752 restraints weight = 23140.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.116490 restraints weight = 12876.775| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3671 r_free = 0.3671 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3671 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14805 Z= 0.118 Angle : 0.601 15.120 20097 Z= 0.295 Chirality : 0.040 0.281 2283 Planarity : 0.004 0.043 2465 Dihedral : 13.019 177.712 2123 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.79 % Allowed : 20.30 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1734 helix: 1.17 (0.15), residues: 1115 sheet: -0.88 (0.63), residues: 56 loop : -1.82 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 221 HIS 0.004 0.001 HIS A 315 PHE 0.033 0.001 PHE B 301 TYR 0.016 0.001 TYR C 546 ARG 0.005 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 2.29795 ( 9) hydrogen bonds : bond 0.03874 ( 890) hydrogen bonds : angle 4.30860 ( 2629) covalent geometry : bond 0.00257 (14802) covalent geometry : angle 0.59905 (20088) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.9100 (t80) cc_final: 0.8884 (t80) REVERT: A 426 PHE cc_start: 0.7338 (t80) cc_final: 0.7006 (t80) REVERT: A 519 MET cc_start: 0.7651 (ttp) cc_final: 0.7352 (ttp) REVERT: B 276 ASN cc_start: 0.7755 (OUTLIER) cc_final: 0.7136 (t0) REVERT: B 300 MET cc_start: 0.8180 (mmt) cc_final: 0.7890 (tpp) REVERT: B 434 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8167 (mm-30) REVERT: B 519 MET cc_start: 0.7320 (mmm) cc_final: 0.7053 (mmt) REVERT: C 175 ILE cc_start: 0.8795 (tp) cc_final: 0.8527 (tp) REVERT: C 188 CYS cc_start: 0.8322 (t) cc_final: 0.7797 (t) REVERT: C 299 ASN cc_start: 0.7507 (m110) cc_final: 0.7055 (p0) REVERT: C 410 ARG cc_start: 0.8645 (mtt90) cc_final: 0.8241 (mtp85) REVERT: C 422 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8946 (tm-30) REVERT: C 573 TYR cc_start: 0.8695 (m-80) cc_final: 0.8366 (m-80) REVERT: C 585 MET cc_start: 0.9017 (mmp) cc_final: 0.8695 (mmp) REVERT: D 330 LYS cc_start: 0.8676 (mmmm) cc_final: 0.7812 (mmmt) REVERT: D 419 GLU cc_start: 0.7609 (pt0) cc_final: 0.7328 (pt0) outliers start: 43 outliers final: 27 residues processed: 235 average time/residue: 0.2351 time to fit residues: 87.0619 Evaluate side-chains 216 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 473 HIS D 339 HIS ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.138225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.107127 restraints weight = 46186.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110862 restraints weight = 20361.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.113316 restraints weight = 12151.075| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14805 Z= 0.174 Angle : 0.648 15.039 20097 Z= 0.318 Chirality : 0.043 0.280 2283 Planarity : 0.004 0.042 2465 Dihedral : 13.003 174.933 2123 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.24 % Allowed : 21.13 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1734 helix: 1.14 (0.15), residues: 1121 sheet: -1.03 (0.61), residues: 56 loop : -1.77 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 221 HIS 0.004 0.001 HIS A 315 PHE 0.038 0.002 PHE B 301 TYR 0.013 0.001 TYR B 354 ARG 0.005 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 3) link_NAG-ASN : angle 2.38107 ( 9) hydrogen bonds : bond 0.04131 ( 890) hydrogen bonds : angle 4.37578 ( 2629) covalent geometry : bond 0.00396 (14802) covalent geometry : angle 0.64592 (20088) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 GLU cc_start: 0.5964 (tt0) cc_final: 0.5572 (tt0) REVERT: B 276 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7095 (t0) REVERT: B 300 MET cc_start: 0.8222 (mmt) cc_final: 0.7952 (tpp) REVERT: B 434 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8255 (mm-30) REVERT: C 175 ILE cc_start: 0.8930 (tp) cc_final: 0.8662 (tp) REVERT: C 188 CYS cc_start: 0.8405 (t) cc_final: 0.7810 (t) REVERT: C 299 ASN cc_start: 0.7592 (m110) cc_final: 0.7147 (p0) REVERT: C 410 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8247 (mtp85) REVERT: C 422 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 573 TYR cc_start: 0.8741 (m-80) cc_final: 0.8368 (m-80) REVERT: C 585 MET cc_start: 0.9052 (mmp) cc_final: 0.8741 (mmp) REVERT: D 405 LEU cc_start: 0.9029 (tp) cc_final: 0.8745 (mp) REVERT: D 419 GLU cc_start: 0.7652 (pt0) cc_final: 0.7399 (pt0) REVERT: D 630 HIS cc_start: 0.7202 (m-70) cc_final: 0.6990 (m-70) outliers start: 50 outliers final: 39 residues processed: 223 average time/residue: 0.2714 time to fit residues: 95.5071 Evaluate side-chains 214 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 501 THR Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 339 HIS Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 15 optimal weight: 0.7980 chunk 125 optimal weight: 0.2980 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 167 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 115 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 473 HIS ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 562 ASN D 339 HIS ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.109644 restraints weight = 45745.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.113481 restraints weight = 19968.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.116014 restraints weight = 11826.036| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14805 Z= 0.121 Angle : 0.617 14.456 20097 Z= 0.302 Chirality : 0.041 0.285 2283 Planarity : 0.004 0.042 2465 Dihedral : 12.962 175.844 2123 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.41 % Allowed : 22.40 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1734 helix: 1.25 (0.15), residues: 1116 sheet: -0.99 (0.60), residues: 56 loop : -1.70 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 171 HIS 0.008 0.001 HIS D 339 PHE 0.031 0.001 PHE B 301 TYR 0.013 0.001 TYR D 483 ARG 0.004 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 3) link_NAG-ASN : angle 2.22654 ( 9) hydrogen bonds : bond 0.03913 ( 890) hydrogen bonds : angle 4.28304 ( 2629) covalent geometry : bond 0.00265 (14802) covalent geometry : angle 0.61521 (20088) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 3.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7318 (t80) cc_final: 0.7103 (t80) REVERT: A 518 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5977 (mt-10) REVERT: B 198 GLU cc_start: 0.5761 (tt0) cc_final: 0.5330 (tt0) REVERT: B 276 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7222 (t0) REVERT: B 300 MET cc_start: 0.8187 (mmt) cc_final: 0.7933 (tpp) REVERT: B 434 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8275 (mm-30) REVERT: B 519 MET cc_start: 0.6897 (mmm) cc_final: 0.6486 (mmt) REVERT: C 175 ILE cc_start: 0.8797 (tp) cc_final: 0.8558 (tp) REVERT: C 188 CYS cc_start: 0.8308 (t) cc_final: 0.7746 (t) REVERT: C 299 ASN cc_start: 0.7526 (m110) cc_final: 0.7101 (p0) REVERT: C 410 ARG cc_start: 0.8631 (mtt90) cc_final: 0.8214 (mtp85) REVERT: C 422 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8933 (tm-30) REVERT: C 573 TYR cc_start: 0.8702 (m-80) cc_final: 0.8328 (m-80) REVERT: C 585 MET cc_start: 0.9022 (mmp) cc_final: 0.8658 (mmp) REVERT: D 330 LYS cc_start: 0.8599 (mmmm) cc_final: 0.7558 (mmtt) REVERT: D 405 LEU cc_start: 0.8975 (tp) cc_final: 0.8704 (mp) REVERT: D 419 GLU cc_start: 0.7644 (pt0) cc_final: 0.7357 (pt0) REVERT: D 539 ARG cc_start: 0.7881 (mmp-170) cc_final: 0.7676 (tpp80) REVERT: D 630 HIS cc_start: 0.7226 (m-70) cc_final: 0.6977 (m-70) outliers start: 37 outliers final: 31 residues processed: 222 average time/residue: 0.3447 time to fit residues: 121.3919 Evaluate side-chains 215 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 2.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 122 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 473 HIS ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.139710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.108533 restraints weight = 53459.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.113404 restraints weight = 22800.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115012 restraints weight = 11936.516| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3631 r_free = 0.3631 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14805 Z= 0.142 Angle : 0.631 14.159 20097 Z= 0.309 Chirality : 0.042 0.286 2283 Planarity : 0.004 0.041 2465 Dihedral : 12.950 175.086 2123 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.54 % Allowed : 22.27 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.20), residues: 1734 helix: 1.27 (0.15), residues: 1116 sheet: -0.30 (0.62), residues: 52 loop : -1.67 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 171 HIS 0.006 0.001 HIS D 339 PHE 0.033 0.001 PHE B 301 TYR 0.015 0.001 TYR C 546 ARG 0.004 0.000 ARG A 274 Details of bonding type rmsd link_NAG-ASN : bond 0.00113 ( 3) link_NAG-ASN : angle 2.24394 ( 9) hydrogen bonds : bond 0.03956 ( 890) hydrogen bonds : angle 4.27298 ( 2629) covalent geometry : bond 0.00321 (14802) covalent geometry : angle 0.62905 (20088) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 426 PHE cc_start: 0.7385 (t80) cc_final: 0.7104 (t80) REVERT: B 198 GLU cc_start: 0.5873 (tt0) cc_final: 0.5407 (tt0) REVERT: B 276 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7108 (t0) REVERT: B 300 MET cc_start: 0.8199 (mmt) cc_final: 0.7955 (tpp) REVERT: B 434 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 519 MET cc_start: 0.6882 (mmm) cc_final: 0.6497 (mmt) REVERT: C 175 ILE cc_start: 0.8824 (tp) cc_final: 0.8574 (tp) REVERT: C 188 CYS cc_start: 0.8342 (t) cc_final: 0.7780 (t) REVERT: C 299 ASN cc_start: 0.7555 (m110) cc_final: 0.7090 (p0) REVERT: C 410 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8209 (mtp85) REVERT: C 422 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8949 (tm-30) REVERT: C 573 TYR cc_start: 0.8658 (m-80) cc_final: 0.8275 (m-80) REVERT: C 585 MET cc_start: 0.9118 (mmp) cc_final: 0.8676 (mmm) REVERT: D 405 LEU cc_start: 0.9057 (tp) cc_final: 0.8760 (mp) REVERT: D 419 GLU cc_start: 0.7731 (pt0) cc_final: 0.7438 (pt0) REVERT: D 539 ARG cc_start: 0.7926 (mmp-170) cc_final: 0.7682 (tpp80) REVERT: D 630 HIS cc_start: 0.7309 (m-70) cc_final: 0.7057 (m-70) outliers start: 39 outliers final: 37 residues processed: 219 average time/residue: 0.2098 time to fit residues: 73.6909 Evaluate side-chains 219 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 260 CYS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 67 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 473 HIS ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 GLN ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.138867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.109685 restraints weight = 39048.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112616 restraints weight = 16779.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.113452 restraints weight = 10604.173| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3636 r_free = 0.3636 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14805 Z= 0.156 Angle : 0.646 14.139 20097 Z= 0.318 Chirality : 0.042 0.283 2283 Planarity : 0.004 0.038 2465 Dihedral : 12.954 174.465 2123 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.79 % Allowed : 22.14 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1734 helix: 1.25 (0.15), residues: 1121 sheet: -0.35 (0.65), residues: 46 loop : -1.67 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 171 HIS 0.006 0.001 HIS D 339 PHE 0.033 0.001 PHE B 301 TYR 0.014 0.001 TYR A 423 ARG 0.004 0.000 ARG B 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 3) link_NAG-ASN : angle 2.25975 ( 9) hydrogen bonds : bond 0.04037 ( 890) hydrogen bonds : angle 4.31892 ( 2629) covalent geometry : bond 0.00355 (14802) covalent geometry : angle 0.64473 (20088) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 ILE cc_start: 0.7296 (OUTLIER) cc_final: 0.6650 (tp) REVERT: A 426 PHE cc_start: 0.7445 (t80) cc_final: 0.7161 (t80) REVERT: B 198 GLU cc_start: 0.6015 (tt0) cc_final: 0.5530 (tt0) REVERT: B 276 ASN cc_start: 0.7743 (OUTLIER) cc_final: 0.7163 (t0) REVERT: B 300 MET cc_start: 0.8190 (mmt) cc_final: 0.7959 (tpp) REVERT: B 434 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8406 (mm-30) REVERT: B 584 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7721 (pp) REVERT: C 175 ILE cc_start: 0.8863 (tp) cc_final: 0.8621 (tp) REVERT: C 188 CYS cc_start: 0.8460 (t) cc_final: 0.7944 (t) REVERT: C 299 ASN cc_start: 0.7551 (m110) cc_final: 0.7106 (p0) REVERT: C 410 ARG cc_start: 0.8665 (mtt90) cc_final: 0.8227 (mtp85) REVERT: C 422 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8956 (tm-30) REVERT: C 573 TYR cc_start: 0.8666 (m-80) cc_final: 0.8280 (m-80) REVERT: C 585 MET cc_start: 0.9125 (mmp) cc_final: 0.8671 (mmm) REVERT: C 593 GLU cc_start: 0.7952 (mp0) cc_final: 0.7509 (mp0) REVERT: D 405 LEU cc_start: 0.9023 (tp) cc_final: 0.8745 (mp) REVERT: D 419 GLU cc_start: 0.7730 (pt0) cc_final: 0.7450 (pt0) REVERT: D 539 ARG cc_start: 0.7954 (mmp-170) cc_final: 0.7723 (tpp80) REVERT: D 630 HIS cc_start: 0.7295 (m-70) cc_final: 0.7041 (m-70) outliers start: 43 outliers final: 35 residues processed: 218 average time/residue: 0.2824 time to fit residues: 102.5136 Evaluate side-chains 219 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 242 HIS Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 403 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 456 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain D residue 233 CYS Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 369 CYS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 536 MET Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 582 VAL Chi-restraints excluded: chain D residue 626 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 2 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 149 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 55 optimal weight: 0.0070 chunk 146 optimal weight: 2.9990 chunk 125 optimal weight: 0.0050 overall best weight: 0.3812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN B 305 ASN B 473 HIS ** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.142489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.111185 restraints weight = 62873.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.116143 restraints weight = 23986.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.118976 restraints weight = 11809.274| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14805 Z= 0.115 Angle : 0.623 14.228 20097 Z= 0.304 Chirality : 0.041 0.262 2283 Planarity : 0.003 0.040 2465 Dihedral : 12.876 175.502 2123 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.46 % Allowed : 23.48 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1734 helix: 1.44 (0.16), residues: 1115 sheet: -0.24 (0.60), residues: 52 loop : -1.62 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 171 HIS 0.007 0.001 HIS D 339 PHE 0.027 0.001 PHE B 301 TYR 0.013 0.001 TYR D 485 ARG 0.005 0.000 ARG B 277 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 3) link_NAG-ASN : angle 2.06696 ( 9) hydrogen bonds : bond 0.03723 ( 890) hydrogen bonds : angle 4.20900 ( 2629) covalent geometry : bond 0.00246 (14802) covalent geometry : angle 0.62123 (20088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6445.49 seconds wall clock time: 117 minutes 15.40 seconds (7035.40 seconds total)