Starting phenix.real_space_refine on Fri Aug 22 17:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9f_35269/08_2025/8i9f_35269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9f_35269/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i9f_35269/08_2025/8i9f_35269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9f_35269/08_2025/8i9f_35269.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i9f_35269/08_2025/8i9f_35269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9f_35269/08_2025/8i9f_35269.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.81, per 1000 atoms: 0.28 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: 0.53 Conformation dependent library (CDL) restraints added in 397.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.22 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: 0.95 Time building geometry restraints manager: 0.72 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: 1.460 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.620 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 115 TYR 0.016 0.001 TYR E 495 PHE 0.009 0.001 PHE E 375 TRP 0.013 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 6594) covalent geometry : angle 0.61849 ( 8953) SS BOND : bond 0.00799 ( 5) SS BOND : angle 2.22977 ( 10) hydrogen bonds : bond 0.14458 ( 265) hydrogen bonds : angle 5.32482 ( 756) link_BETA1-4 : bond 0.00403 ( 6) link_BETA1-4 : angle 2.45680 ( 18) link_NAG-ASN : bond 0.00339 ( 7) link_NAG-ASN : angle 2.22941 ( 21) *********************** 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 : 0.254 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: 0.5319 time to fit residues: 54.5164 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 : 0.267 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.105585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.076962 restraints weight = 9948.734| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.57 r_work: 0.2758 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.0911 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= 0.144 Angle : 0.582 9.221 9002 Z= 0.295 Chirality : 0.046 0.260 965 Planarity : 0.004 0.035 1141 Dihedral : 7.979 57.295 1133 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.11 % Allowed : 21.31 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.29), residues: 756 helix: -0.26 (0.27), residues: 366 sheet: -0.63 (0.73), residues: 46 loop : -2.14 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 192 TYR 0.016 0.001 TYR E 495 PHE 0.011 0.001 PHE E 464 TRP 0.012 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 6594) covalent geometry : angle 0.56513 ( 8953) SS BOND : bond 0.00757 ( 5) SS BOND : angle 1.90856 ( 10) hydrogen bonds : bond 0.05278 ( 265) hydrogen bonds : angle 4.06623 ( 756) link_BETA1-4 : bond 0.00344 ( 6) link_BETA1-4 : angle 2.11374 ( 18) link_NAG-ASN : bond 0.00282 ( 7) link_NAG-ASN : angle 1.85776 ( 21) *********************** 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 99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 58 time to evaluate : 0.258 Fit side-chains REVERT: A 31 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7839 (tttm) REVERT: A 86 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8357 (pm20) REVERT: A 366 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8278 (ttt) REVERT: A 401 HIS cc_start: 0.8812 (OUTLIER) cc_final: 0.8440 (m-70) REVERT: E 358 ILE cc_start: 0.3919 (OUTLIER) cc_final: 0.3500 (mt) REVERT: E 420 ASP cc_start: 0.8534 (m-30) cc_final: 0.8125 (m-30) REVERT: E 498 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7704 (mtt90) outliers start: 41 outliers final: 14 residues processed: 93 average time/residue: 0.6439 time to fit residues: 62.7499 Evaluate side-chains 75 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 86 GLN 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 12 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 34 optimal weight: 8.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.107335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.078808 restraints weight = 9890.479| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.59 r_work: 0.2789 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1229 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= 0.124 Angle : 0.556 9.518 9002 Z= 0.278 Chirality : 0.044 0.259 965 Planarity : 0.003 0.034 1141 Dihedral : 6.542 56.708 1113 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.07 % Allowed : 22.95 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.30), residues: 756 helix: 0.25 (0.28), residues: 370 sheet: -0.21 (0.78), residues: 46 loop : -1.84 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 192 TYR 0.013 0.001 TYR E 495 PHE 0.016 0.001 PHE E 375 TRP 0.011 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6594) covalent geometry : angle 0.53984 ( 8953) SS BOND : bond 0.01008 ( 5) SS BOND : angle 1.79461 ( 10) hydrogen bonds : bond 0.04677 ( 265) hydrogen bonds : angle 3.92175 ( 756) link_BETA1-4 : bond 0.00474 ( 6) link_BETA1-4 : angle 2.09170 ( 18) link_NAG-ASN : bond 0.00251 ( 7) link_NAG-ASN : angle 1.78920 ( 21) *********************** 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 93 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 59 time to evaluate : 0.322 Fit side-chains REVERT: A 31 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7732 (tttm) REVERT: A 366 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8352 (ttt) REVERT: A 401 HIS cc_start: 0.8900 (OUTLIER) cc_final: 0.8522 (m-70) REVERT: E 340 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6308 (pm20) REVERT: E 358 ILE cc_start: 0.3889 (OUTLIER) cc_final: 0.3461 (mt) REVERT: E 420 ASP cc_start: 0.8541 (m-30) cc_final: 0.8090 (m-30) REVERT: E 444 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7847 (ttmt) REVERT: E 498 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7827 (mtt90) outliers start: 34 outliers final: 17 residues processed: 89 average time/residue: 0.6216 time to fit residues: 58.0033 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 : 0.266 ------------------------------------------------------------------------------- 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 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 444 LYS 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 52 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 0.0030 chunk 58 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.107434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.078893 restraints weight = 9919.135| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.58 r_work: 0.2795 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6612 Z= 0.121 Angle : 0.556 9.569 9002 Z= 0.276 Chirality : 0.045 0.259 965 Planarity : 0.003 0.034 1141 Dihedral : 6.231 57.079 1113 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.02 % Allowed : 24.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.31), residues: 756 helix: 0.51 (0.28), residues: 371 sheet: -0.27 (0.79), residues: 46 loop : -1.69 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.012 0.001 TYR E 495 PHE 0.017 0.001 PHE E 375 TRP 0.010 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6594) covalent geometry : angle 0.54043 ( 8953) SS BOND : bond 0.01278 ( 5) SS BOND : angle 1.72875 ( 10) hydrogen bonds : bond 0.04531 ( 265) hydrogen bonds : angle 3.88071 ( 756) link_BETA1-4 : bond 0.00468 ( 6) link_BETA1-4 : angle 2.02784 ( 18) link_NAG-ASN : bond 0.00240 ( 7) link_NAG-ASN : angle 1.76492 ( 21) *********************** 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 82 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.251 Fit side-chains REVERT: A 31 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7663 (tttm) REVERT: A 366 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8345 (ttt) REVERT: A 401 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8534 (m-70) REVERT: A 421 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7692 (mm) REVERT: E 340 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6304 (pm20) REVERT: E 420 ASP cc_start: 0.8521 (m-30) cc_final: 0.8069 (m-30) REVERT: E 444 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7815 (ttmt) REVERT: E 498 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7786 (mtt90) outliers start: 27 outliers final: 14 residues processed: 78 average time/residue: 0.6495 time to fit residues: 53.1487 Evaluate side-chains 71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 366 MET Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE 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 444 LYS 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 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 58 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 287 GLN A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.079453 restraints weight = 9961.976| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.59 r_work: 0.2800 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1525 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= 0.114 Angle : 0.562 9.585 9002 Z= 0.277 Chirality : 0.045 0.281 965 Planarity : 0.003 0.033 1141 Dihedral : 5.966 57.037 1110 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.17 % Allowed : 24.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.31), residues: 756 helix: 0.82 (0.28), residues: 362 sheet: -0.22 (0.78), residues: 47 loop : -1.53 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 192 TYR 0.011 0.001 TYR E 495 PHE 0.009 0.001 PHE A 315 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 6594) covalent geometry : angle 0.54069 ( 8953) SS BOND : bond 0.01068 ( 5) SS BOND : angle 2.97124 ( 10) hydrogen bonds : bond 0.04342 ( 265) hydrogen bonds : angle 3.83556 ( 756) link_BETA1-4 : bond 0.00466 ( 6) link_BETA1-4 : angle 2.01810 ( 18) link_NAG-ASN : bond 0.00241 ( 7) link_NAG-ASN : angle 1.75272 ( 21) *********************** 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 79 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.266 Fit side-chains REVERT: A 31 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7618 (tttm) REVERT: A 401 HIS cc_start: 0.8877 (OUTLIER) cc_final: 0.8535 (m-70) REVERT: A 421 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7599 (mm) REVERT: E 340 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: E 420 ASP cc_start: 0.8466 (m-30) cc_final: 0.8009 (m-30) REVERT: E 444 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7837 (ttmt) REVERT: E 498 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7774 (mtt90) outliers start: 28 outliers final: 15 residues processed: 76 average time/residue: 0.6183 time to fit residues: 49.3687 Evaluate side-chains 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 421 ILE 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 445 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.108623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.080161 restraints weight = 10010.769| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.59 r_work: 0.2809 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1663 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= 0.112 Angle : 0.569 9.582 9002 Z= 0.282 Chirality : 0.044 0.302 965 Planarity : 0.003 0.033 1141 Dihedral : 5.794 57.161 1110 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.32 % Allowed : 24.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.31), residues: 756 helix: 0.87 (0.28), residues: 370 sheet: -0.14 (0.77), residues: 47 loop : -1.55 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 559 TYR 0.011 0.001 TYR E 495 PHE 0.008 0.001 PHE A 315 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 6594) covalent geometry : angle 0.54736 ( 8953) SS BOND : bond 0.01041 ( 5) SS BOND : angle 3.09321 ( 10) hydrogen bonds : bond 0.04210 ( 265) hydrogen bonds : angle 3.77843 ( 756) link_BETA1-4 : bond 0.00446 ( 6) link_BETA1-4 : angle 1.99641 ( 18) link_NAG-ASN : bond 0.00236 ( 7) link_NAG-ASN : angle 1.73003 ( 21) *********************** 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 79 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 50 time to evaluate : 0.245 Fit side-chains REVERT: A 31 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: A 401 HIS cc_start: 0.8847 (OUTLIER) cc_final: 0.8522 (m-70) REVERT: E 340 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: E 420 ASP cc_start: 0.8440 (m-30) cc_final: 0.7973 (m-30) REVERT: E 444 LYS cc_start: 0.8084 (mtmm) cc_final: 0.7867 (ttmt) REVERT: E 498 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7797 (mtt90) outliers start: 29 outliers final: 19 residues processed: 75 average time/residue: 0.5986 time to fit residues: 47.2988 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 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 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 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 493 GLN 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 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3392 r_free = 0.3392 target = 0.108563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080202 restraints weight = 9962.512| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.58 r_work: 0.2814 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1731 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= 0.118 Angle : 0.582 10.589 9002 Z= 0.288 Chirality : 0.045 0.350 965 Planarity : 0.004 0.080 1141 Dihedral : 5.716 57.222 1110 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.17 % Allowed : 25.19 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.31), residues: 756 helix: 1.00 (0.28), residues: 370 sheet: -0.12 (0.80), residues: 47 loop : -1.48 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 460 TYR 0.011 0.001 TYR E 495 PHE 0.009 0.001 PHE A 32 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6594) covalent geometry : angle 0.55749 ( 8953) SS BOND : bond 0.01125 ( 5) SS BOND : angle 3.65196 ( 10) hydrogen bonds : bond 0.04278 ( 265) hydrogen bonds : angle 3.80380 ( 756) link_BETA1-4 : bond 0.00450 ( 6) link_BETA1-4 : angle 1.97145 ( 18) link_NAG-ASN : bond 0.00228 ( 7) link_NAG-ASN : angle 1.73238 ( 21) *********************** 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 79 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.250 Fit side-chains REVERT: A 31 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7586 (tttm) REVERT: A 192 ARG cc_start: 0.8381 (mtm-85) cc_final: 0.8155 (mtt180) REVERT: A 401 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8530 (m-70) REVERT: A 421 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7599 (mm) REVERT: E 340 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: E 358 ILE cc_start: 0.3087 (OUTLIER) cc_final: 0.2629 (mt) REVERT: E 420 ASP cc_start: 0.8436 (m-30) cc_final: 0.7992 (m-30) REVERT: E 444 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7857 (ttmt) REVERT: E 498 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7807 (mtt90) outliers start: 28 outliers final: 18 residues processed: 75 average time/residue: 0.6336 time to fit residues: 49.9417 Evaluate side-chains 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 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 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 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 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.107228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.078741 restraints weight = 9914.200| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.58 r_work: 0.2783 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6612 Z= 0.147 Angle : 0.628 17.926 9002 Z= 0.310 Chirality : 0.047 0.393 965 Planarity : 0.004 0.073 1141 Dihedral : 5.791 57.597 1110 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.62 % Allowed : 24.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.31), residues: 756 helix: 1.10 (0.28), residues: 365 sheet: -0.07 (0.80), residues: 47 loop : -1.40 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.016 0.001 TYR A 202 PHE 0.012 0.001 PHE A 32 TRP 0.009 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 6594) covalent geometry : angle 0.59866 ( 8953) SS BOND : bond 0.01347 ( 5) SS BOND : angle 4.60427 ( 10) hydrogen bonds : bond 0.04807 ( 265) hydrogen bonds : angle 3.80332 ( 756) link_BETA1-4 : bond 0.00430 ( 6) link_BETA1-4 : angle 1.94639 ( 18) link_NAG-ASN : bond 0.00208 ( 7) link_NAG-ASN : angle 1.74944 ( 21) *********************** 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 83 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 0.249 Fit side-chains REVERT: A 31 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7673 (tttm) REVERT: A 192 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8138 (mtt180) REVERT: A 332 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8028 (ttm) REVERT: A 401 HIS cc_start: 0.8928 (OUTLIER) cc_final: 0.8503 (m-70) REVERT: E 340 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: E 358 ILE cc_start: 0.2865 (OUTLIER) cc_final: 0.2381 (mt) REVERT: E 420 ASP cc_start: 0.8448 (m-30) cc_final: 0.7984 (m-30) REVERT: E 444 LYS cc_start: 0.8044 (mtmm) cc_final: 0.7811 (ttmt) REVERT: E 498 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7670 (mtt90) outliers start: 31 outliers final: 20 residues processed: 77 average time/residue: 0.6290 time to fit residues: 50.8251 Evaluate side-chains 74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 434 ILE Chi-restraints excluded: chain E residue 440 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 45 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.080245 restraints weight = 10087.356| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.60 r_work: 0.2810 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1839 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= 0.116 Angle : 0.624 19.256 9002 Z= 0.308 Chirality : 0.045 0.335 965 Planarity : 0.004 0.065 1141 Dihedral : 5.613 57.955 1109 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.62 % Allowed : 25.34 % Favored : 70.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.31), residues: 756 helix: 1.24 (0.28), residues: 365 sheet: -0.01 (0.81), residues: 47 loop : -1.37 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.016 0.001 TYR A 202 PHE 0.008 0.001 PHE A 32 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6594) covalent geometry : angle 0.59518 ( 8953) SS BOND : bond 0.01162 ( 5) SS BOND : angle 4.48649 ( 10) hydrogen bonds : bond 0.04263 ( 265) hydrogen bonds : angle 3.78581 ( 756) link_BETA1-4 : bond 0.00457 ( 6) link_BETA1-4 : angle 1.97583 ( 18) link_NAG-ASN : bond 0.00232 ( 7) link_NAG-ASN : angle 1.72835 ( 21) *********************** 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 79 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 48 time to evaluate : 0.268 Fit side-chains REVERT: A 31 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7570 (tttm) REVERT: A 192 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8163 (mtt180) REVERT: A 332 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8019 (ttm) REVERT: A 401 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8394 (m-70) REVERT: A 421 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7642 (mm) REVERT: E 340 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6205 (pm20) REVERT: E 420 ASP cc_start: 0.8446 (m-30) cc_final: 0.7989 (m-30) REVERT: E 444 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7836 (ttmt) REVERT: E 498 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7694 (mtt90) outliers start: 31 outliers final: 16 residues processed: 75 average time/residue: 0.6474 time to fit residues: 50.9606 Evaluate side-chains 69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 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 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 445 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 65 optimal weight: 0.0020 chunk 31 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.108406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.079843 restraints weight = 9856.327| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.58 r_work: 0.2808 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1860 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= 0.127 Angle : 0.646 17.902 9002 Z= 0.320 Chirality : 0.046 0.348 965 Planarity : 0.004 0.063 1141 Dihedral : 5.667 58.285 1109 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.58 % Allowed : 25.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.31), residues: 756 helix: 1.24 (0.28), residues: 366 sheet: -0.03 (0.80), residues: 47 loop : -1.36 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.016 0.001 TYR A 202 PHE 0.020 0.001 PHE E 375 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6594) covalent geometry : angle 0.61329 ( 8953) SS BOND : bond 0.01160 ( 5) SS BOND : angle 5.10109 ( 10) hydrogen bonds : bond 0.04467 ( 265) hydrogen bonds : angle 3.77191 ( 756) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.95255 ( 18) link_NAG-ASN : bond 0.00249 ( 7) link_NAG-ASN : angle 1.73628 ( 21) ********************** 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 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.261 Fit side-chains REVERT: A 31 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7625 (tttm) REVERT: A 142 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7494 (pt) REVERT: A 192 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.8183 (mtt180) REVERT: A 332 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7980 (ttm) REVERT: A 401 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8544 (m-70) REVERT: A 421 ILE cc_start: 0.7936 (OUTLIER) cc_final: 0.7677 (mm) REVERT: E 340 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6215 (pm20) REVERT: E 420 ASP cc_start: 0.8467 (m-30) cc_final: 0.8021 (m-30) REVERT: E 434 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7558 (mp) REVERT: E 444 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7839 (ttmt) REVERT: E 498 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7721 (mtt90) outliers start: 24 outliers final: 15 residues processed: 69 average time/residue: 0.6282 time to fit residues: 45.6932 Evaluate side-chains 69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 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 445 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 23 optimal weight: 0.0870 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.080325 restraints weight = 9961.183| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.59 r_work: 0.2816 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6612 Z= 0.122 Angle : 0.645 16.903 9002 Z= 0.321 Chirality : 0.045 0.262 965 Planarity : 0.004 0.058 1141 Dihedral : 5.672 58.791 1109 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.43 % Allowed : 25.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.31), residues: 756 helix: 1.31 (0.28), residues: 366 sheet: 0.60 (0.82), residues: 42 loop : -1.47 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 559 TYR 0.016 0.001 TYR A 202 PHE 0.009 0.001 PHE A 32 TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6594) covalent geometry : angle 0.61154 ( 8953) SS BOND : bond 0.00734 ( 5) SS BOND : angle 5.20821 ( 10) hydrogen bonds : bond 0.04313 ( 265) hydrogen bonds : angle 3.77788 ( 756) link_BETA1-4 : bond 0.00448 ( 6) link_BETA1-4 : angle 1.96622 ( 18) link_NAG-ASN : bond 0.00229 ( 7) link_NAG-ASN : angle 1.71448 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.39 seconds wall clock time: 44 minutes 25.35 seconds (2665.35 seconds total)