Starting phenix.real_space_refine on Tue Mar 11 17:11:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i9f_35269/03_2025/8i9f_35269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i9f_35269/03_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_35269/03_2025/8i9f_35269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i9f_35269/03_2025/8i9f_35269.map" model { file = "/net/cci-nas-00/data/ceres_data/8i9f_35269/03_2025/8i9f_35269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i9f_35269/03_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-5624/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: 4.48, per 1000 atoms: 0.70 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: 1.70 Conformation dependent library (CDL) restraints added in 864.1 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: 0.73 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: 2.03 Time building geometry restraints manager: 2.00 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: 1.390 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.180 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.350 ------------------------------------------------------------------------------- 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 6594 Z= 0.262 Angle : 0.618 6.628 8953 Z= 0.341 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 *********************** 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 : 0.703 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: 1.1343 time to fit residues: 116.5334 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 : 0.844 ------------------------------------------------------------------------------- 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 6594 Z= 0.215 Angle : 0.563 9.235 8953 Z= 0.289 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 *********************** 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 : 0.776 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: 1.2901 time to fit residues: 124.9291 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 : 0.795 ------------------------------------------------------------------------------- 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 6594 Z= 0.190 Angle : 0.541 9.465 8953 Z= 0.274 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 *********************** 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 : 0.707 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: 1.1836 time to fit residues: 106.1303 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 : 0.709 ------------------------------------------------------------------------------- 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 6594 Z= 0.171 Angle : 0.532 9.570 8953 Z= 0.267 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 *********************** 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 : 0.734 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: 1.2259 time to fit residues: 102.1527 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 : 0.761 ------------------------------------------------------------------------------- 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: 0.1980 chunk 15 optimal weight: 2.9990 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: 0.4320 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.108965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.080597 restraints weight = 9895.852| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.58 r_work: 0.2821 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6594 Z= 0.144 Angle : 0.533 9.899 8953 Z= 0.266 Chirality : 0.044 0.303 965 Planarity : 0.003 0.033 1141 Dihedral : 5.884 57.063 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 : 3.87 % Allowed : 24.59 % 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: -0.47 (0.31), residues: 756 helix: 0.79 (0.28), residues: 370 sheet: -0.17 (0.79), residues: 46 loop : -1.60 (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 0.009 0.001 TYR E 495 ARG 0.001 0.000 ARG A 192 *********************** 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: 26 poor density : 54 time to evaluate : 0.786 Fit side-chains REVERT: A 31 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7561 (tttm) REVERT: A 62 MET cc_start: 0.7890 (ptm) cc_final: 0.7668 (ptm) REVERT: A 150 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 401 HIS cc_start: 0.8811 (OUTLIER) cc_final: 0.8477 (m-70) REVERT: A 472 GLN cc_start: 0.8669 (mt0) cc_final: 0.8441 (mt0) REVERT: E 420 ASP cc_start: 0.8475 (m-30) cc_final: 0.8014 (m-30) REVERT: E 498 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7847 (mtt90) outliers start: 26 outliers final: 14 residues processed: 76 average time/residue: 1.3681 time to fit residues: 109.6182 Evaluate side-chains 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 54 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 47 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 69 optimal weight: 0.0570 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.109663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.081450 restraints weight = 9816.101| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.56 r_work: 0.2826 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6594 Z= 0.145 Angle : 0.535 9.701 8953 Z= 0.265 Chirality : 0.044 0.300 965 Planarity : 0.003 0.033 1141 Dihedral : 5.664 57.267 1110 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.17 % Allowed : 24.89 % Favored : 70.94 % 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: -0.22 (0.31), residues: 756 helix: 1.02 (0.28), residues: 370 sheet: -0.08 (0.78), residues: 47 loop : -1.50 (0.33), residues: 339 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 0.008 0.001 PHE A 315 TYR 0.009 0.001 TYR E 495 ARG 0.001 0.000 ARG A 245 *********************** 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 83 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.757 Fit side-chains REVERT: A 31 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7409 (tttm) REVERT: A 62 MET cc_start: 0.7859 (ptm) cc_final: 0.7607 (ptm) REVERT: A 150 GLU cc_start: 0.8322 (tm-30) cc_final: 0.8049 (tm-30) REVERT: A 401 HIS cc_start: 0.8777 (OUTLIER) cc_final: 0.8431 (m-70) REVERT: A 472 GLN cc_start: 0.8653 (mt0) cc_final: 0.8408 (mt0) REVERT: E 340 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6269 (pm20) REVERT: E 420 ASP cc_start: 0.8420 (m-30) cc_final: 0.7959 (m-30) REVERT: E 498 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7821 (mtt90) outliers start: 28 outliers final: 15 residues processed: 79 average time/residue: 1.2696 time to fit residues: 105.5966 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 : 0.800 ------------------------------------------------------------------------------- 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 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 350 VAL 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 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: 6.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 68 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 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 = 0.108806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.080432 restraints weight = 9893.139| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.58 r_work: 0.2818 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6594 Z= 0.175 Angle : 0.553 10.614 8953 Z= 0.277 Chirality : 0.045 0.327 965 Planarity : 0.004 0.078 1141 Dihedral : 5.631 57.380 1110 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % 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: -0.12 (0.31), residues: 756 helix: 1.10 (0.28), residues: 370 sheet: 0.03 (0.79), residues: 47 loop : -1.47 (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 0.018 0.001 PHE E 375 TYR 0.016 0.001 TYR A 202 ARG 0.001 0.000 ARG A 192 *********************** 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 81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 0.737 Fit side-chains REVERT: A 31 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7577 (tttm) REVERT: A 62 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7662 (ptm) REVERT: A 332 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8013 (ttm) REVERT: A 401 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8505 (m-70) REVERT: A 472 GLN cc_start: 0.8677 (mt0) cc_final: 0.8448 (mt0) REVERT: E 340 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6253 (pm20) REVERT: E 358 ILE cc_start: 0.2905 (OUTLIER) cc_final: 0.2416 (mt) REVERT: E 420 ASP cc_start: 0.8421 (m-30) cc_final: 0.7961 (m-30) REVERT: E 434 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7533 (mp) REVERT: E 498 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7857 (mtt90) outliers start: 31 outliers final: 15 residues processed: 75 average time/residue: 1.3391 time to fit residues: 105.5662 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 : 0.765 ------------------------------------------------------------------------------- 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 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 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 462 LYS 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: 0.9980 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 63 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.080001 restraints weight = 9853.361| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.58 r_work: 0.2800 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6594 Z= 0.187 Angle : 0.582 17.339 8953 Z= 0.290 Chirality : 0.046 0.390 965 Planarity : 0.004 0.074 1141 Dihedral : 5.643 57.349 1110 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.87 % Allowed : 25.48 % 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: -0.11 (0.31), residues: 756 helix: 1.10 (0.28), residues: 373 sheet: 0.08 (0.79), residues: 47 loop : -1.49 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.010 0.001 PHE A 32 TYR 0.017 0.001 TYR A 202 ARG 0.006 0.000 ARG A 192 *********************** 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 76 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.757 Fit side-chains REVERT: A 31 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7597 (tttm) REVERT: A 62 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7662 (ptm) REVERT: A 332 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7996 (ttm) REVERT: A 401 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8536 (m-70) REVERT: A 421 ILE cc_start: 0.7894 (OUTLIER) cc_final: 0.7636 (mm) REVERT: A 472 GLN cc_start: 0.8694 (mt0) cc_final: 0.8461 (mt0) REVERT: E 340 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6238 (pm20) REVERT: E 358 ILE cc_start: 0.2746 (OUTLIER) cc_final: 0.2251 (mt) REVERT: E 420 ASP cc_start: 0.8428 (m-30) cc_final: 0.7986 (m-30) REVERT: E 434 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7546 (mp) REVERT: E 498 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7917 (mtt90) outliers start: 26 outliers final: 12 residues processed: 73 average time/residue: 1.1892 time to fit residues: 92.0288 Evaluate side-chains 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 330 ASN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.081835 restraints weight = 9843.079| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.58 r_work: 0.2840 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6594 Z= 0.145 Angle : 0.589 19.158 8953 Z= 0.293 Chirality : 0.044 0.311 965 Planarity : 0.004 0.067 1141 Dihedral : 5.541 57.376 1110 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.43 % Allowed : 26.08 % Favored : 70.49 % 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: 0.07 (0.31), residues: 756 helix: 1.29 (0.28), residues: 371 sheet: 0.07 (0.82), residues: 47 loop : -1.41 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE A 327 TYR 0.017 0.001 TYR A 202 ARG 0.005 0.000 ARG A 192 *********************** 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 72 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.708 Fit side-chains REVERT: A 31 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7384 (tttm) REVERT: A 62 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7670 (ptm) REVERT: A 365 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (p) REVERT: A 401 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8509 (m-70) REVERT: A 472 GLN cc_start: 0.8668 (mt0) cc_final: 0.8439 (mt0) REVERT: E 340 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6224 (pm20) REVERT: E 358 ILE cc_start: 0.2853 (OUTLIER) cc_final: 0.2410 (mt) REVERT: E 420 ASP cc_start: 0.8414 (m-30) cc_final: 0.7940 (m-30) REVERT: E 498 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7841 (mtt90) outliers start: 23 outliers final: 10 residues processed: 69 average time/residue: 1.1477 time to fit residues: 83.8206 Evaluate side-chains 64 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 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 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 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: 1.9990 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 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 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 = 0.3395 r_free = 0.3395 target = 0.108870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.080260 restraints weight = 9932.248| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.60 r_work: 0.2814 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6594 Z= 0.187 Angle : 0.629 19.034 8953 Z= 0.315 Chirality : 0.046 0.340 965 Planarity : 0.004 0.062 1141 Dihedral : 5.450 57.471 1107 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.43 % Allowed : 25.78 % 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: -0.01 (0.31), residues: 756 helix: 1.22 (0.28), residues: 375 sheet: -0.13 (0.80), residues: 47 loop : -1.45 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.004 0.001 HIS A 241 PHE 0.011 0.001 PHE A 32 TYR 0.017 0.001 TYR A 202 ARG 0.005 0.000 ARG A 192 ********************** 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 73 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.702 Fit side-chains REVERT: A 31 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7588 (tttm) REVERT: A 62 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7704 (ptm) REVERT: A 332 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8037 (ttm) REVERT: A 365 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 401 HIS cc_start: 0.8843 (OUTLIER) cc_final: 0.8538 (m-70) REVERT: A 421 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7680 (mm) REVERT: A 472 GLN cc_start: 0.8689 (mt0) cc_final: 0.8457 (mt0) REVERT: E 358 ILE cc_start: 0.2790 (OUTLIER) cc_final: 0.2384 (mt) REVERT: E 420 ASP cc_start: 0.8451 (m-30) cc_final: 0.8015 (m-30) REVERT: E 498 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7740 (mtt90) outliers start: 23 outliers final: 10 residues processed: 69 average time/residue: 1.2028 time to fit residues: 87.7580 Evaluate side-chains 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 581 VAL 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 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: 0.0470 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 0.0040 chunk 56 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.0770 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.2248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 325 GLN A 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.112620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.084728 restraints weight = 10002.590| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.51 r_work: 0.2881 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 6594 Z= 0.138 Angle : 0.613 18.576 8953 Z= 0.303 Chirality : 0.043 0.269 965 Planarity : 0.004 0.057 1141 Dihedral : 5.338 57.645 1107 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.38 % Allowed : 27.27 % Favored : 70.34 % 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: 0.22 (0.32), residues: 756 helix: 1.50 (0.28), residues: 372 sheet: 0.02 (0.82), residues: 47 loop : -1.44 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.008 0.001 PHE A 315 TYR 0.016 0.001 TYR A 202 ARG 0.005 0.000 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5039.85 seconds wall clock time: 86 minutes 31.56 seconds (5191.56 seconds total)