Starting phenix.real_space_refine on Sun Apr 27 18:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9f_35269/04_2025/8i9f_35269.cif" } resolution = 2.9 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 33 5.16 5 C 4106 2.51 5 N 1047 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6415 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Chain: "E" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1363 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.94, per 1000 atoms: 0.61 Number of scatterers: 6415 At special positions: 0 Unit cell: (106.526, 88.047, 106.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 33 16.00 O 1229 8.00 N 1047 7.00 C 4106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A 701 " - " ASN A 322 " " NAG B 1 " - " ASN A 53 " " NAG C 1 " - " ASN A 90 " " NAG D 1 " - " ASN A 103 " " NAG F 1 " - " ASN A 432 " " NAG G 1 " - " ASN A 546 " " NAG H 1 " - " ASN E 343 " Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 807.1 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1440 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 6 sheets defined 52.1% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 removed outlier: 3.647A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.061A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA A 65 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.562A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.859A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.628A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.558A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 3.858A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.975A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 234 " --> pdb=" O PHE A 230 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.788A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.639A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 299 Processing helix chain 'A' and resid 305 through 318 removed outlier: 3.782A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.512A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 331' Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.916A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.717A pdb=" N ARG A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.613A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.670A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.660A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.046A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 532 " --> pdb=" O ALA A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.852A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.601A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 removed outlier: 3.561A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.864A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 356 removed outlier: 3.748A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 265 hydrogen bonds defined for protein. 756 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: 1.71 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2025 1.35 - 1.47: 1795 1.47 - 1.59: 2720 1.59 - 1.72: 0 1.72 - 1.84: 54 Bond restraints: 6594 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.58e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 6589 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 8532 1.33 - 2.65: 338 2.65 - 3.98: 67 3.98 - 5.30: 11 5.30 - 6.63: 5 Bond angle restraints: 8953 Sorted by residual: angle pdb=" N VAL A 172 " pdb=" CA VAL A 172 " pdb=" C VAL A 172 " ideal model delta sigma weight residual 111.90 109.01 2.89 8.10e-01 1.52e+00 1.27e+01 angle pdb=" C ASN A 338 " pdb=" CA ASN A 338 " pdb=" CB ASN A 338 " ideal model delta sigma weight residual 110.96 115.69 -4.73 1.54e+00 4.22e-01 9.43e+00 angle pdb=" N GLY A 147 " pdb=" CA GLY A 147 " pdb=" C GLY A 147 " ideal model delta sigma weight residual 113.18 119.55 -6.37 2.37e+00 1.78e-01 7.22e+00 angle pdb=" CA ASN A 338 " pdb=" C ASN A 338 " pdb=" N VAL A 339 " ideal model delta sigma weight residual 116.92 119.94 -3.02 1.16e+00 7.43e-01 6.77e+00 angle pdb=" CA GLN A 325 " pdb=" CB GLN A 325 " pdb=" CG GLN A 325 " ideal model delta sigma weight residual 114.10 119.10 -5.00 2.00e+00 2.50e-01 6.25e+00 ... (remaining 8948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3478 17.58 - 35.17: 402 35.17 - 52.75: 123 52.75 - 70.34: 28 70.34 - 87.92: 10 Dihedral angle restraints: 4041 sinusoidal: 1798 harmonic: 2243 Sorted by residual: dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -32.29 -53.71 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CA THR A 20 " pdb=" C THR A 20 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA VAL A 339 " pdb=" C VAL A 339 " pdb=" N GLN A 340 " pdb=" CA GLN A 340 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 4038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 830 0.067 - 0.133: 131 0.133 - 0.200: 3 0.200 - 0.267: 0 0.267 - 0.333: 1 Chirality restraints: 965 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C4 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" C5 NAG D 1 " pdb=" O4 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.36 -0.17 2.00e-01 2.50e+01 7.15e-01 ... (remaining 962 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 583 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.026 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO A 235 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 320 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A 321 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.019 5.00e-02 4.00e+02 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 631 2.74 - 3.28: 6045 3.28 - 3.82: 9854 3.82 - 4.36: 12385 4.36 - 4.90: 21634 Nonbonded interactions: 50549 Sorted by model distance: nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.204 3.040 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.204 3.040 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.236 3.040 nonbonded pdb=" OH TYR A 237 " pdb=" O VAL A 485 " model vdw 2.286 3.040 nonbonded pdb=" OE1 GLU A 231 " pdb=" NZ LYS A 234 " model vdw 2.383 3.120 ... (remaining 50544 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.004 0.038 6612 Z= 0.188 Angle : 0.640 8.085 9002 Z= 0.346 Chirality : 0.047 0.333 965 Planarity : 0.004 0.040 1141 Dihedral : 16.782 87.920 2586 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.11 % Rotamer: Outliers : 5.51 % Allowed : 21.46 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.26), residues: 756 helix: -1.22 (0.25), residues: 359 sheet: -1.39 (0.67), residues: 46 loop : -2.70 (0.27), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE E 375 TYR 0.016 0.001 TYR E 495 ARG 0.002 0.000 ARG A 115 Details of bonding type rmsd link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 2.22941 ( 21) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 2.45680 ( 18) hydrogen bonds : bond 0.14458 ( 265) hydrogen bonds : angle 5.32482 ( 756) SS BOND : bond 0.00799 ( 5) SS BOND : angle 2.22977 ( 10) covalent geometry : bond 0.00405 ( 6594) covalent geometry : angle 0.61849 ( 8953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.692 Fit side-chains REVERT: A 109 SER cc_start: 0.7989 (OUTLIER) cc_final: 0.7674 (p) REVERT: A 114 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8121 (ttmm) REVERT: E 340 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6370 (pm20) REVERT: E 358 ILE cc_start: 0.3999 (OUTLIER) cc_final: 0.3617 (mt) outliers start: 37 outliers final: 18 residues processed: 97 average time/residue: 1.0314 time to fit residues: 106.1343 Evaluate side-chains 77 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 408 SER Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 493 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 HIS A 58 ASN A 137 ASN A 154 ASN A 210 ASN A 338 ASN A 340 GLN A 378 HIS A 401 HIS A 472 GLN A 493 HIS A 505 HIS A 586 ASN A 601 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.105728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.077202 restraints weight = 9803.424| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.56 r_work: 0.2767 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6612 Z= 0.142 Angle : 0.579 9.235 9002 Z= 0.293 Chirality : 0.046 0.250 965 Planarity : 0.004 0.035 1141 Dihedral : 7.876 57.296 1133 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.96 % Allowed : 21.31 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.29), residues: 756 helix: -0.20 (0.27), residues: 364 sheet: -0.61 (0.73), residues: 46 loop : -2.14 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.012 0.001 PHE E 464 TYR 0.016 0.001 TYR E 495 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 7) link_NAG-ASN : angle 1.83065 ( 21) link_BETA1-4 : bond 0.00502 ( 6) link_BETA1-4 : angle 2.06767 ( 18) hydrogen bonds : bond 0.05209 ( 265) hydrogen bonds : angle 4.04980 ( 756) SS BOND : bond 0.00551 ( 5) SS BOND : angle 1.90539 ( 10) covalent geometry : bond 0.00332 ( 6594) covalent geometry : angle 0.56274 ( 8953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.723 Fit side-chains REVERT: A 31 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7841 (tttm) REVERT: A 150 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 366 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8264 (ttt) REVERT: A 401 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8431 (m-70) REVERT: E 358 ILE cc_start: 0.3966 (OUTLIER) cc_final: 0.3536 (mt) REVERT: E 420 ASP cc_start: 0.8531 (m-30) cc_final: 0.8127 (m-30) REVERT: E 498 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7707 (mtt90) outliers start: 40 outliers final: 13 residues processed: 92 average time/residue: 1.2142 time to fit residues: 117.5906 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.078123 restraints weight = 9901.566| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.58 r_work: 0.2784 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6612 Z= 0.127 Angle : 0.559 9.465 9002 Z= 0.279 Chirality : 0.045 0.263 965 Planarity : 0.003 0.034 1141 Dihedral : 6.556 56.785 1113 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.92 % Allowed : 22.95 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.30), residues: 756 helix: 0.24 (0.27), residues: 370 sheet: -0.22 (0.78), residues: 46 loop : -1.85 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE E 375 TYR 0.013 0.001 TYR E 495 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 7) link_NAG-ASN : angle 1.79911 ( 21) link_BETA1-4 : bond 0.00444 ( 6) link_BETA1-4 : angle 2.10069 ( 18) hydrogen bonds : bond 0.04773 ( 265) hydrogen bonds : angle 3.92700 ( 756) SS BOND : bond 0.00903 ( 5) SS BOND : angle 1.99863 ( 10) covalent geometry : bond 0.00294 ( 6594) covalent geometry : angle 0.54149 ( 8953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.708 Fit side-chains REVERT: A 31 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7705 (tttm) REVERT: A 62 MET cc_start: 0.7908 (ptm) cc_final: 0.7699 (ptm) REVERT: A 150 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8011 (tm-30) REVERT: A 366 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8335 (ttt) REVERT: A 401 HIS cc_start: 0.8882 (OUTLIER) cc_final: 0.8508 (m-70) REVERT: E 340 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6302 (pm20) REVERT: E 358 ILE cc_start: 0.3860 (OUTLIER) cc_final: 0.3427 (mt) REVERT: E 420 ASP cc_start: 0.8511 (m-30) cc_final: 0.8091 (m-30) REVERT: E 498 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7762 (mtt90) outliers start: 33 outliers final: 18 residues processed: 85 average time/residue: 1.1847 time to fit residues: 106.3233 Evaluate side-chains 75 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 54 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.107528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.078959 restraints weight = 9962.391| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.59 r_work: 0.2796 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6612 Z= 0.114 Angle : 0.547 9.570 9002 Z= 0.271 Chirality : 0.044 0.260 965 Planarity : 0.003 0.033 1141 Dihedral : 6.197 57.067 1113 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.02 % Allowed : 24.74 % Favored : 71.24 % 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: -0.67 (0.31), residues: 756 helix: 0.59 (0.28), residues: 368 sheet: -0.14 (0.75), residues: 46 loop : -1.67 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.018 0.001 PHE E 375 TYR 0.011 0.001 TYR E 495 ARG 0.002 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 7) link_NAG-ASN : angle 1.75786 ( 21) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 2.02963 ( 18) hydrogen bonds : bond 0.04426 ( 265) hydrogen bonds : angle 3.81598 ( 756) SS BOND : bond 0.00982 ( 5) SS BOND : angle 1.49960 ( 10) covalent geometry : bond 0.00262 ( 6594) covalent geometry : angle 0.53227 ( 8953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 54 time to evaluate : 0.659 Fit side-chains REVERT: A 31 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7644 (tttm) REVERT: A 62 MET cc_start: 0.7868 (ptm) cc_final: 0.7631 (ptm) REVERT: A 150 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 401 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8517 (m-70) REVERT: A 421 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7609 (mm) REVERT: E 340 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: E 420 ASP cc_start: 0.8520 (m-30) cc_final: 0.8083 (m-30) REVERT: E 498 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7788 (mtt90) outliers start: 27 outliers final: 14 residues processed: 79 average time/residue: 1.1490 time to fit residues: 95.6935 Evaluate side-chains 70 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 chunk 54 optimal weight: 0.0980 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080319 restraints weight = 9894.046| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.57 r_work: 0.2814 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6612 Z= 0.104 Angle : 0.558 9.879 9002 Z= 0.273 Chirality : 0.044 0.276 965 Planarity : 0.003 0.033 1141 Dihedral : 5.894 57.071 1110 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.02 % Allowed : 24.44 % Favored : 71.54 % 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: -0.48 (0.31), residues: 756 helix: 0.78 (0.28), residues: 370 sheet: -0.17 (0.79), residues: 46 loop : -1.61 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.018 0.001 PHE E 375 TYR 0.010 0.001 TYR E 495 ARG 0.001 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 7) link_NAG-ASN : angle 1.74462 ( 21) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 2.02638 ( 18) hydrogen bonds : bond 0.04113 ( 265) hydrogen bonds : angle 3.82066 ( 756) SS BOND : bond 0.00455 ( 5) SS BOND : angle 2.98014 ( 10) covalent geometry : bond 0.00232 ( 6594) covalent geometry : angle 0.53652 ( 8953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.798 Fit side-chains REVERT: A 31 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7579 (tttm) REVERT: A 62 MET cc_start: 0.7891 (ptm) cc_final: 0.7669 (ptm) REVERT: A 150 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 401 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8494 (m-70) REVERT: E 340 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6355 (pm20) REVERT: E 420 ASP cc_start: 0.8475 (m-30) cc_final: 0.8010 (m-30) REVERT: E 498 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7845 (mtt90) outliers start: 27 outliers final: 14 residues processed: 76 average time/residue: 1.5640 time to fit residues: 124.2945 Evaluate side-chains 68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 62 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.080341 restraints weight = 9827.267| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.56 r_work: 0.2806 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6612 Z= 0.113 Angle : 0.566 10.005 9002 Z= 0.277 Chirality : 0.045 0.306 965 Planarity : 0.003 0.033 1141 Dihedral : 5.743 57.178 1110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.62 % Allowed : 24.59 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.29 (0.31), residues: 756 helix: 0.94 (0.28), residues: 370 sheet: -0.11 (0.77), residues: 47 loop : -1.52 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR E 495 ARG 0.001 0.000 ARG A 460 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 7) link_NAG-ASN : angle 1.72503 ( 21) link_BETA1-4 : bond 0.00490 ( 6) link_BETA1-4 : angle 1.97356 ( 18) hydrogen bonds : bond 0.04197 ( 265) hydrogen bonds : angle 3.76351 ( 756) SS BOND : bond 0.00777 ( 5) SS BOND : angle 3.07028 ( 10) covalent geometry : bond 0.00258 ( 6594) covalent geometry : angle 0.54518 ( 8953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 53 time to evaluate : 1.121 Fit side-chains REVERT: A 31 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7566 (tttm) REVERT: A 62 MET cc_start: 0.7886 (ptm) cc_final: 0.7642 (ptm) REVERT: A 150 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8068 (tm-30) REVERT: A 401 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8513 (m-70) REVERT: A 421 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 472 GLN cc_start: 0.8688 (mt0) cc_final: 0.8460 (mt0) REVERT: E 340 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: E 420 ASP cc_start: 0.8425 (m-30) cc_final: 0.7959 (m-30) REVERT: E 498 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7825 (mtt90) outliers start: 31 outliers final: 16 residues processed: 80 average time/residue: 1.8365 time to fit residues: 154.5390 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 61 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.106780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.078280 restraints weight = 9926.039| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.57 r_work: 0.2782 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6612 Z= 0.154 Angle : 0.608 11.024 9002 Z= 0.301 Chirality : 0.047 0.357 965 Planarity : 0.004 0.079 1141 Dihedral : 5.824 57.205 1110 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.62 % Allowed : 24.29 % Favored : 71.09 % 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: -0.21 (0.31), residues: 756 helix: 1.01 (0.28), residues: 365 sheet: -0.02 (0.78), residues: 47 loop : -1.45 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.001 PHE A 32 TYR 0.014 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 7) link_NAG-ASN : angle 1.75957 ( 21) link_BETA1-4 : bond 0.00417 ( 6) link_BETA1-4 : angle 1.94077 ( 18) hydrogen bonds : bond 0.04907 ( 265) hydrogen bonds : angle 3.79213 ( 756) SS BOND : bond 0.01097 ( 5) SS BOND : angle 3.82536 ( 10) covalent geometry : bond 0.00368 ( 6594) covalent geometry : angle 0.58338 ( 8953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 51 time to evaluate : 1.095 Fit side-chains REVERT: A 31 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7697 (tttm) REVERT: A 62 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7689 (ptm) REVERT: A 192 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8121 (mtt180) REVERT: A 332 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7987 (ttm) REVERT: A 401 HIS cc_start: 0.8963 (OUTLIER) cc_final: 0.8615 (m-70) REVERT: E 340 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6213 (pm20) REVERT: E 358 ILE cc_start: 0.2971 (OUTLIER) cc_final: 0.2495 (mt) REVERT: E 420 ASP cc_start: 0.8464 (m-30) cc_final: 0.8028 (m-30) REVERT: E 498 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7700 (mtt90) outliers start: 31 outliers final: 18 residues processed: 76 average time/residue: 1.8851 time to fit residues: 151.7533 Evaluate side-chains 74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 48 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.108561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.080216 restraints weight = 9857.738| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.57 r_work: 0.2808 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6612 Z= 0.114 Angle : 0.606 17.688 9002 Z= 0.298 Chirality : 0.045 0.378 965 Planarity : 0.004 0.072 1141 Dihedral : 5.719 57.601 1110 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.32 % Allowed : 25.34 % Favored : 70.34 % 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: -0.06 (0.31), residues: 756 helix: 1.15 (0.28), residues: 366 sheet: 0.11 (0.79), residues: 47 loop : -1.41 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.019 0.001 PHE E 375 TYR 0.010 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 7) link_NAG-ASN : angle 1.72316 ( 21) link_BETA1-4 : bond 0.00455 ( 6) link_BETA1-4 : angle 1.99562 ( 18) hydrogen bonds : bond 0.04250 ( 265) hydrogen bonds : angle 3.77470 ( 756) SS BOND : bond 0.01235 ( 5) SS BOND : angle 4.47642 ( 10) covalent geometry : bond 0.00258 ( 6594) covalent geometry : angle 0.57561 ( 8953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 1.925 Fit side-chains REVERT: A 31 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7563 (tttm) REVERT: A 62 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7677 (ptm) REVERT: A 192 ARG cc_start: 0.8373 (mtm-85) cc_final: 0.8128 (mtt180) REVERT: A 332 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7985 (ttm) REVERT: A 401 HIS cc_start: 0.8865 (OUTLIER) cc_final: 0.8439 (m-70) REVERT: A 421 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7631 (mm) REVERT: E 340 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: E 358 ILE cc_start: 0.2722 (OUTLIER) cc_final: 0.2224 (mt) REVERT: E 420 ASP cc_start: 0.8437 (m-30) cc_final: 0.8003 (m-30) REVERT: E 498 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7888 (mtt90) outliers start: 29 outliers final: 14 residues processed: 77 average time/residue: 1.8626 time to fit residues: 150.7202 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.078849 restraints weight = 9895.172| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.58 r_work: 0.2792 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6612 Z= 0.141 Angle : 0.631 18.986 9002 Z= 0.311 Chirality : 0.046 0.348 965 Planarity : 0.004 0.068 1141 Dihedral : 5.639 57.906 1108 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.73 % Allowed : 25.63 % Favored : 70.64 % 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: -0.08 (0.31), residues: 756 helix: 1.14 (0.28), residues: 366 sheet: -0.14 (0.79), residues: 47 loop : -1.39 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.019 0.001 PHE E 375 TYR 0.013 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 7) link_NAG-ASN : angle 1.75054 ( 21) link_BETA1-4 : bond 0.00430 ( 6) link_BETA1-4 : angle 1.95452 ( 18) hydrogen bonds : bond 0.04683 ( 265) hydrogen bonds : angle 3.78022 ( 756) SS BOND : bond 0.01199 ( 5) SS BOND : angle 4.67637 ( 10) covalent geometry : bond 0.00334 ( 6594) covalent geometry : angle 0.60065 ( 8953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.752 Fit side-chains REVERT: A 31 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7663 (tttm) REVERT: A 62 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7707 (ptm) REVERT: A 192 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.8073 (mtt180) REVERT: A 332 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7978 (ttm) REVERT: A 401 HIS cc_start: 0.8912 (OUTLIER) cc_final: 0.8445 (m-70) REVERT: A 421 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7686 (mm) REVERT: E 340 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6187 (pm20) REVERT: E 420 ASP cc_start: 0.8442 (m-30) cc_final: 0.7961 (m-30) REVERT: E 498 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7691 (mtt90) outliers start: 25 outliers final: 14 residues processed: 71 average time/residue: 1.2264 time to fit residues: 91.9209 Evaluate side-chains 68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 47 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 481 ASN Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 34 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.108777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080212 restraints weight = 9922.442| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.58 r_work: 0.2807 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6612 Z= 0.115 Angle : 0.630 18.600 9002 Z= 0.310 Chirality : 0.046 0.328 965 Planarity : 0.004 0.062 1141 Dihedral : 5.631 58.328 1108 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.28 % Allowed : 26.08 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.03 (0.31), residues: 756 helix: 1.27 (0.28), residues: 366 sheet: -0.16 (0.79), residues: 47 loop : -1.37 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE E 375 TYR 0.010 0.001 TYR E 495 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 7) link_NAG-ASN : angle 1.71289 ( 21) link_BETA1-4 : bond 0.00461 ( 6) link_BETA1-4 : angle 1.98012 ( 18) hydrogen bonds : bond 0.04277 ( 265) hydrogen bonds : angle 3.76365 ( 756) SS BOND : bond 0.00940 ( 5) SS BOND : angle 5.26273 ( 10) covalent geometry : bond 0.00258 ( 6594) covalent geometry : angle 0.59448 ( 8953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.683 Fit side-chains REVERT: A 31 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7567 (tttm) REVERT: A 62 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7682 (ptm) REVERT: A 192 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.8075 (mtt180) REVERT: A 332 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7992 (ttm) REVERT: A 365 THR cc_start: 0.8531 (m) cc_final: 0.8279 (p) REVERT: A 401 HIS cc_start: 0.8869 (OUTLIER) cc_final: 0.8565 (m-70) REVERT: A 421 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7647 (mm) REVERT: E 340 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: E 420 ASP cc_start: 0.8439 (m-30) cc_final: 0.7991 (m-30) REVERT: E 498 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7716 (mtt90) outliers start: 22 outliers final: 14 residues processed: 67 average time/residue: 1.2499 time to fit residues: 88.2297 Evaluate side-chains 69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 380 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 493 GLN Chi-restraints excluded: chain E residue 498 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 56 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.109594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.080999 restraints weight = 10063.426| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.61 r_work: 0.2824 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6612 Z= 0.109 Angle : 0.611 16.117 9002 Z= 0.301 Chirality : 0.044 0.261 965 Planarity : 0.004 0.058 1141 Dihedral : 5.537 58.752 1108 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.13 % Allowed : 26.08 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: 0.04 (0.31), residues: 756 helix: 1.32 (0.28), residues: 371 sheet: -0.14 (0.80), residues: 47 loop : -1.48 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.010 0.001 PHE E 375 TYR 0.018 0.001 TYR A 202 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 7) link_NAG-ASN : angle 1.69003 ( 21) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 1.95435 ( 18) hydrogen bonds : bond 0.04098 ( 265) hydrogen bonds : angle 3.73001 ( 756) SS BOND : bond 0.00621 ( 5) SS BOND : angle 5.23616 ( 10) covalent geometry : bond 0.00239 ( 6594) covalent geometry : angle 0.57456 ( 8953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5417.70 seconds wall clock time: 96 minutes 10.30 seconds (5770.30 seconds total)