Starting phenix.real_space_refine on Thu Nov 14 13:22:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_35269.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_35269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_35269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_35269.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9f_35269/11_2024/8i9f_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-5513/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: 4.57, per 1000 atoms: 0.71 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: 1.64 Conformation dependent library (CDL) restraints added in 834.0 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: 1.84 Time building geometry restraints manager: 1.89 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: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.640 Find NCS groups from input model: 0.080 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:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.800 ------------------------------------------------------------------------------- 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 : 0.723 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: 1.0496 time to fit residues: 108.0155 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 : 0.721 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.720 Fit side-chains REVERT: A 31 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7623 (tttm) REVERT: A 366 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7931 (ttt) REVERT: A 401 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.8435 (m-70) REVERT: E 358 ILE cc_start: 0.3910 (OUTLIER) cc_final: 0.3422 (mt) REVERT: E 420 ASP cc_start: 0.8350 (m-30) cc_final: 0.7964 (m-30) REVERT: E 498 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7766 (mtt90) outliers start: 40 outliers final: 13 residues processed: 92 average time/residue: 1.2352 time to fit residues: 119.6372 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 : 0.735 ------------------------------------------------------------------------------- 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 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.1980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1223 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= 0.166 Angle : 0.532 9.508 8953 Z= 0.270 Chirality : 0.044 0.259 965 Planarity : 0.003 0.033 1141 Dihedral : 6.551 56.750 1113 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.62 % Allowed : 23.25 % 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: -1.02 (0.30), residues: 756 helix: 0.29 (0.28), residues: 367 sheet: -0.21 (0.78), residues: 46 loop : -1.84 (0.31), residues: 343 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 0.016 0.001 PHE E 375 TYR 0.011 0.001 TYR E 495 ARG 0.002 0.000 ARG A 460 *********************** 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 89 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 58 time to evaluate : 0.718 Fit side-chains REVERT: A 31 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7476 (tttm) REVERT: A 366 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8006 (ttt) REVERT: A 401 HIS cc_start: 0.8799 (OUTLIER) cc_final: 0.8420 (m-70) REVERT: E 358 ILE cc_start: 0.3743 (OUTLIER) cc_final: 0.3381 (mt) REVERT: E 420 ASP cc_start: 0.8343 (m-30) cc_final: 0.7918 (m-30) REVERT: E 498 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7839 (mtt90) outliers start: 31 outliers final: 17 residues processed: 84 average time/residue: 1.2356 time to fit residues: 109.3753 Evaluate side-chains 74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 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 67 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.0270 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1419 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= 0.163 Angle : 0.525 9.548 8953 Z= 0.264 Chirality : 0.044 0.262 965 Planarity : 0.003 0.033 1141 Dihedral : 6.182 57.079 1112 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.73 % Allowed : 24.59 % Favored : 71.68 % 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: -0.68 (0.31), residues: 756 helix: 0.60 (0.28), residues: 368 sheet: -0.11 (0.76), residues: 46 loop : -1.70 (0.32), residues: 342 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 0.017 0.001 PHE E 375 TYR 0.011 0.001 TYR E 495 ARG 0.001 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 79 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.735 Fit side-chains REVERT: A 31 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7393 (tttm) REVERT: A 401 HIS cc_start: 0.8789 (OUTLIER) cc_final: 0.8456 (m-70) REVERT: E 340 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6341 (pm20) REVERT: E 420 ASP cc_start: 0.8341 (m-30) cc_final: 0.7914 (m-30) REVERT: E 498 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7884 (mtt90) outliers start: 25 outliers final: 13 residues processed: 77 average time/residue: 1.2299 time to fit residues: 99.8545 Evaluate side-chains 68 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 483 VAL 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 41 optimal weight: 0.0770 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 0.0770 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.0980 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6594 Z= 0.134 Angle : 0.528 9.598 8953 Z= 0.264 Chirality : 0.043 0.275 965 Planarity : 0.003 0.032 1141 Dihedral : 5.841 57.119 1110 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.17 % Allowed : 23.85 % 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 (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: -0.45 (0.31), residues: 756 helix: 0.83 (0.28), residues: 370 sheet: -0.14 (0.80), residues: 46 loop : -1.61 (0.32), residues: 340 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 0.019 0.001 PHE E 375 TYR 0.009 0.001 TYR A 50 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 81 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 53 time to evaluate : 0.755 Fit side-chains REVERT: A 31 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7297 (tttm) REVERT: A 401 HIS cc_start: 0.8761 (OUTLIER) cc_final: 0.8368 (m-70) REVERT: A 472 GLN cc_start: 0.8420 (mt0) cc_final: 0.8196 (mt0) REVERT: E 340 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.6338 (pm20) REVERT: E 420 ASP cc_start: 0.8308 (m-30) cc_final: 0.7861 (m-30) REVERT: E 498 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7903 (mtt90) outliers start: 28 outliers final: 13 residues processed: 76 average time/residue: 1.3476 time to fit residues: 107.7958 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 : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 340 GLU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 440 LYS Chi-restraints excluded: chain E residue 443 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 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 65 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6594 Z= 0.167 Angle : 0.541 9.905 8953 Z= 0.270 Chirality : 0.044 0.294 965 Planarity : 0.003 0.033 1141 Dihedral : 5.708 57.304 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 : 3.73 % Allowed : 25.04 % 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: -0.26 (0.31), residues: 756 helix: 0.99 (0.28), residues: 370 sheet: -0.12 (0.79), residues: 46 loop : -1.51 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.004 0.001 HIS A 374 PHE 0.009 0.001 PHE A 32 TYR 0.011 0.001 TYR E 495 ARG 0.003 0.000 ARG A 559 *********************** 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 78 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.740 Fit side-chains REVERT: A 31 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7351 (tttm) REVERT: A 401 HIS cc_start: 0.8817 (OUTLIER) cc_final: 0.8450 (m-70) REVERT: A 472 GLN cc_start: 0.8459 (mt0) cc_final: 0.8245 (mt0) REVERT: E 340 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: E 420 ASP cc_start: 0.8304 (m-30) cc_final: 0.7848 (m-30) REVERT: E 498 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7927 (mtt90) outliers start: 25 outliers final: 16 residues processed: 74 average time/residue: 1.1988 time to fit residues: 93.8297 Evaluate side-chains 69 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 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 462 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 52 optimal weight: 0.2980 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6594 Z= 0.152 Angle : 0.548 10.353 8953 Z= 0.276 Chirality : 0.044 0.343 965 Planarity : 0.004 0.080 1141 Dihedral : 5.594 57.304 1110 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.77 % Allowed : 24.59 % 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: -0.10 (0.31), residues: 756 helix: 1.15 (0.28), residues: 370 sheet: -0.04 (0.79), residues: 47 loop : -1.48 (0.33), residues: 339 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 0.018 0.001 PHE E 375 TYR 0.015 0.001 TYR A 202 ARG 0.001 0.000 ARG A 460 *********************** 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 84 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.771 Fit side-chains REVERT: A 31 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7197 (tttm) REVERT: A 332 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7546 (ttm) REVERT: A 365 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8512 (p) REVERT: A 401 HIS cc_start: 0.8772 (OUTLIER) cc_final: 0.8402 (m-70) REVERT: A 421 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7686 (mm) REVERT: A 472 GLN cc_start: 0.8450 (mt0) cc_final: 0.8241 (mt0) REVERT: E 358 ILE cc_start: 0.3005 (OUTLIER) cc_final: 0.2575 (mt) REVERT: E 420 ASP cc_start: 0.8284 (m-30) cc_final: 0.7824 (m-30) REVERT: E 498 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7945 (mtt90) outliers start: 32 outliers final: 15 residues processed: 80 average time/residue: 1.4877 time to fit residues: 125.1250 Evaluate side-chains 71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 49 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 350 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 443 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 65 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 374 HIS E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6594 Z= 0.170 Angle : 0.569 17.566 8953 Z= 0.285 Chirality : 0.045 0.388 965 Planarity : 0.004 0.073 1141 Dihedral : 5.423 57.383 1108 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.73 % Allowed : 25.63 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.31), residues: 756 helix: 1.21 (0.28), residues: 370 sheet: -0.06 (0.78), residues: 47 loop : -1.46 (0.32), residues: 339 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 0.009 0.001 PHE A 32 TYR 0.017 0.001 TYR A 202 ARG 0.001 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: 25 poor density : 51 time to evaluate : 0.661 Fit side-chains REVERT: A 31 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7339 (tttm) REVERT: A 401 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8498 (m-70) REVERT: A 421 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7765 (mm) REVERT: A 472 GLN cc_start: 0.8455 (mt0) cc_final: 0.8241 (mt0) REVERT: E 358 ILE cc_start: 0.2860 (OUTLIER) cc_final: 0.2416 (mt) REVERT: E 420 ASP cc_start: 0.8269 (m-30) cc_final: 0.7809 (m-30) REVERT: E 498 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7951 (mtt90) outliers start: 25 outliers final: 13 residues processed: 74 average time/residue: 1.3591 time to fit residues: 106.5352 Evaluate side-chains 63 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 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 350 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6594 Z= 0.222 Angle : 0.626 19.655 8953 Z= 0.315 Chirality : 0.047 0.354 965 Planarity : 0.004 0.068 1141 Dihedral : 5.459 57.362 1107 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.58 % Allowed : 25.78 % 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: -0.01 (0.31), residues: 756 helix: 1.24 (0.28), residues: 366 sheet: -0.13 (0.80), residues: 47 loop : -1.40 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.019 0.001 PHE E 375 TYR 0.018 0.001 TYR A 202 ARG 0.002 0.000 ARG A 161 *********************** 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 71 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.709 Fit side-chains REVERT: A 31 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7439 (tttm) REVERT: A 360 MET cc_start: 0.8554 (ptt) cc_final: 0.8051 (ptt) REVERT: A 401 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.8595 (m-70) REVERT: E 358 ILE cc_start: 0.2736 (OUTLIER) cc_final: 0.2276 (mt) REVERT: E 420 ASP cc_start: 0.8290 (m-30) cc_final: 0.7826 (m-30) REVERT: E 498 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7829 (mtt90) outliers start: 24 outliers final: 14 residues processed: 69 average time/residue: 1.1580 time to fit residues: 84.9453 Evaluate side-chains 64 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 A residue 547 SER 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 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: 3.9990 chunk 49 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6594 Z= 0.195 Angle : 0.632 20.565 8953 Z= 0.316 Chirality : 0.046 0.331 965 Planarity : 0.004 0.062 1141 Dihedral : 5.537 57.788 1107 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.83 % Allowed : 26.53 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.31), residues: 756 helix: 1.29 (0.28), residues: 366 sheet: -0.18 (0.79), residues: 47 loop : -1.38 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.020 0.001 PHE E 375 TYR 0.017 0.001 TYR A 202 ARG 0.001 0.000 ARG A 460 ********************** 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 67 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.776 Fit side-chains REVERT: A 31 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7401 (tttm) REVERT: A 360 MET cc_start: 0.8502 (ptt) cc_final: 0.7982 (ptt) REVERT: A 401 HIS cc_start: 0.8894 (OUTLIER) cc_final: 0.8445 (m-70) REVERT: A 421 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7777 (mm) REVERT: E 420 ASP cc_start: 0.8277 (m-30) cc_final: 0.7814 (m-30) REVERT: E 498 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7814 (mtt90) outliers start: 19 outliers final: 12 residues processed: 65 average time/residue: 1.1748 time to fit residues: 80.8602 Evaluate side-chains 60 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS 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 421 ILE Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 581 VAL 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 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 54 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 61 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.108993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.080437 restraints weight = 9812.216| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.58 r_work: 0.2815 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1955 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= 0.176 Angle : 0.619 17.479 8953 Z= 0.309 Chirality : 0.045 0.262 965 Planarity : 0.004 0.056 1141 Dihedral : 5.532 58.306 1107 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.53 % Allowed : 26.97 % Favored : 70.49 % 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: -0.02 (0.31), residues: 756 helix: 1.27 (0.28), residues: 374 sheet: -0.14 (0.80), residues: 47 loop : -1.53 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE E 375 TYR 0.017 0.001 TYR A 202 ARG 0.001 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2606.09 seconds wall clock time: 47 minutes 24.61 seconds (2844.61 seconds total)