Starting phenix.real_space_refine on Mon Mar 11 00:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9e_35268/03_2024/8i9e_35268.pdb" } resolution = 3.2 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= 0.002 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 4107 2.51 5 N 1050 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6421 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: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1369 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: 4.06, per 1000 atoms: 0.63 Number of scatterers: 6421 At special positions: 0 Unit cell: (105.12, 87.6, 107.31, 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 1231 8.00 N 1050 7.00 C 4107 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=2.05 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=2.02 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 - 3.50 Amino acid : False - 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: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds 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 5 sheets defined 50.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 21 through 52 removed outlier: 3.560A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 80 removed outlier: 4.208A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.062A 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 91 through 101 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.537A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.213A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.092A 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 231 removed outlier: 4.089A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 3.951A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.862A 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 319 removed outlier: 3.796A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.523A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.107A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.677A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 4.275A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 447 removed outlier: 4.087A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.963A 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: 4.163A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.665A 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: 3.813A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 removed outlier: 3.912A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 599 Proline residue: A 590 - end of helix Processing helix chain 'E' and resid 339 through 344 removed outlier: 4.144A pdb=" N ASN E 343 " --> pdb=" O ASP E 339 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 344 " --> pdb=" O GLU E 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 339 through 344' Processing helix chain 'E' and resid 365 through 370 removed outlier: 4.227A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 365 through 370' Processing helix chain 'E' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.774A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.004A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 357 through 358 removed outlier: 3.609A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 254 hydrogen bonds defined for protein. 729 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: 1.57 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2016 1.34 - 1.45: 1252 1.45 - 1.57: 3277 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 6599 Sorted by residual: bond pdb=" C ASN A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.314 0.020 8.40e-03 1.42e+04 5.68e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 1.531 1.554 -0.023 1.51e-02 4.39e+03 2.40e+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 2.31e+00 bond pdb=" C1 NAG A 701 " pdb=" O5 NAG A 701 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 ... (remaining 6594 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.26: 169 106.26 - 113.22: 3478 113.22 - 120.17: 2615 120.17 - 127.13: 2601 127.13 - 134.09: 97 Bond angle restraints: 8960 Sorted by residual: angle pdb=" N CYS A 133 " pdb=" CA CYS A 133 " pdb=" C CYS A 133 " ideal model delta sigma weight residual 109.85 115.18 -5.33 1.58e+00 4.01e-01 1.14e+01 angle pdb=" N SER A 331 " pdb=" CA SER A 331 " pdb=" C SER A 331 " ideal model delta sigma weight residual 110.50 114.99 -4.49 1.41e+00 5.03e-01 1.02e+01 angle pdb=" N ASN A 149 " pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 113.02 109.81 3.21 1.20e+00 6.94e-01 7.18e+00 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 113.18 106.96 6.22 2.37e+00 1.78e-01 6.90e+00 angle pdb=" CA PRO A 146 " pdb=" C PRO A 146 " pdb=" O PRO A 146 " ideal model delta sigma weight residual 123.07 119.70 3.37 1.38e+00 5.25e-01 5.95e+00 ... (remaining 8955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 3494 17.38 - 34.76: 398 34.76 - 52.14: 118 52.14 - 69.52: 30 69.52 - 86.90: 6 Dihedral angle restraints: 4046 sinusoidal: 1803 harmonic: 2243 Sorted by residual: dihedral pdb=" CA VAL E 341 " pdb=" C VAL E 341 " pdb=" N PHE E 342 " pdb=" CA PHE E 342 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 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 -46.70 -39.30 1 1.00e+01 1.00e-02 2.17e+01 dihedral pdb=" CA PHE E 490 " pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta harmonic sigma weight residual -180.00 -162.31 -17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 872 0.085 - 0.170: 89 0.170 - 0.255: 3 0.255 - 0.339: 0 0.339 - 0.424: 2 Chirality restraints: 966 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 343 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 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 -2.02 -0.38 2.00e-01 2.50e+01 3.65e+00 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 -2.29 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 963 not shown) Planarity restraints: 1150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 583 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 428 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C PHE A 428 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE A 428 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 429 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " -0.029 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO A 235 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " -0.024 5.00e-02 4.00e+02 ... (remaining 1147 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1786 2.79 - 3.32: 5522 3.32 - 3.85: 9679 3.85 - 4.37: 11320 4.37 - 4.90: 20040 Nonbonded interactions: 48347 Sorted by model distance: nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR E 500 " model vdw 2.266 2.440 nonbonded pdb=" N ASP A 136 " pdb=" OD1 ASP A 136 " model vdw 2.304 2.520 nonbonded pdb=" N GLU A 430 " pdb=" OE1 GLU A 430 " model vdw 2.305 2.520 nonbonded pdb=" OG SER E 438 " pdb=" OD2 ASP E 442 " model vdw 2.315 2.440 nonbonded pdb=" O SER A 19 " pdb=" OG SER A 19 " model vdw 2.332 2.440 ... (remaining 48342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.540 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: 5.200 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 : 0.008 0.054 6599 Z= 0.544 Angle : 0.743 7.052 8960 Z= 0.404 Chirality : 0.054 0.424 966 Planarity : 0.004 0.050 1143 Dihedral : 16.266 86.905 2591 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.76 % Allowed : 16.37 % Favored : 78.87 % 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: -3.37 (0.27), residues: 756 helix: -1.00 (0.26), residues: 353 sheet: -1.92 (0.70), residues: 41 loop : -3.68 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.012 0.002 PHE A 274 TYR 0.017 0.002 TYR A 183 ARG 0.004 0.001 ARG A 245 *********************** 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 99 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 67 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 416 LYS cc_start: 0.8423 (tppt) cc_final: 0.7528 (tptt) REVERT: E 353 TRP cc_start: 0.8192 (OUTLIER) cc_final: 0.7517 (p-90) REVERT: E 423 TYR cc_start: 0.8252 (t80) cc_final: 0.7702 (t80) REVERT: E 471 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7165 (tt0) outliers start: 32 outliers final: 20 residues processed: 96 average time/residue: 0.1656 time to fit residues: 22.1400 Evaluate side-chains 83 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 542 CYS Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 353 TRP Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 210 ASN A 239 HIS A 472 GLN A 493 HIS A 505 HIS A 508 ASN E 477 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6599 Z= 0.165 Angle : 0.565 9.544 8960 Z= 0.282 Chirality : 0.044 0.295 966 Planarity : 0.004 0.038 1143 Dihedral : 8.584 57.616 1142 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.72 % Allowed : 18.60 % Favored : 77.68 % 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: -1.93 (0.30), residues: 756 helix: 0.31 (0.29), residues: 351 sheet: -1.21 (0.73), residues: 41 loop : -3.05 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE E 377 TYR 0.009 0.001 TYR A 158 ARG 0.002 0.000 ARG A 245 *********************** 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 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 66 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8547 (tmm) cc_final: 0.8262 (tmm) REVERT: A 416 LYS cc_start: 0.8302 (tppt) cc_final: 0.7468 (tptt) REVERT: E 423 TYR cc_start: 0.8189 (t80) cc_final: 0.7570 (t80) REVERT: E 471 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7077 (mm-30) outliers start: 25 outliers final: 16 residues processed: 84 average time/residue: 0.1719 time to fit residues: 20.2854 Evaluate side-chains 77 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 535 HIS A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6599 Z= 0.179 Angle : 0.538 9.417 8960 Z= 0.269 Chirality : 0.044 0.281 966 Planarity : 0.004 0.034 1143 Dihedral : 7.077 56.775 1120 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.57 % Allowed : 19.64 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.31), residues: 756 helix: 0.81 (0.29), residues: 353 sheet: -0.72 (0.74), residues: 41 loop : -2.69 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 478 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8561 (tmm) cc_final: 0.8252 (tmm) REVERT: A 416 LYS cc_start: 0.8356 (tppt) cc_final: 0.7478 (tptt) REVERT: A 480 MET cc_start: 0.8806 (mtp) cc_final: 0.8573 (mtm) REVERT: A 489 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: E 423 TYR cc_start: 0.8192 (t80) cc_final: 0.7676 (t80) REVERT: E 471 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7062 (mm-30) outliers start: 24 outliers final: 19 residues processed: 89 average time/residue: 0.1536 time to fit residues: 19.4567 Evaluate side-chains 85 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 0.0040 chunk 72 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6599 Z= 0.179 Angle : 0.525 9.450 8960 Z= 0.261 Chirality : 0.044 0.288 966 Planarity : 0.003 0.032 1143 Dihedral : 6.642 57.311 1117 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.02 % Allowed : 20.09 % Favored : 75.89 % 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: -1.00 (0.31), residues: 756 helix: 1.00 (0.29), residues: 354 sheet: -0.61 (0.75), residues: 41 loop : -2.52 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 417 PHE 0.010 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG A 460 *********************** 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 91 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.728 Fit side-chains REVERT: A 190 MET cc_start: 0.8560 (tmm) cc_final: 0.8224 (tmm) REVERT: A 416 LYS cc_start: 0.8300 (tppt) cc_final: 0.7426 (tptt) REVERT: A 480 MET cc_start: 0.8805 (mtp) cc_final: 0.8575 (mtm) REVERT: A 489 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.7093 (pm20) REVERT: E 423 TYR cc_start: 0.8178 (t80) cc_final: 0.7629 (t80) REVERT: E 471 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6981 (mm-30) outliers start: 27 outliers final: 22 residues processed: 84 average time/residue: 0.1442 time to fit residues: 17.6662 Evaluate side-chains 85 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 62 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 29 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7895 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6599 Z= 0.173 Angle : 0.524 9.450 8960 Z= 0.259 Chirality : 0.045 0.284 966 Planarity : 0.003 0.032 1143 Dihedral : 6.329 57.301 1113 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 4.32 % Allowed : 20.68 % Favored : 75.00 % 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: -0.83 (0.31), residues: 756 helix: 1.14 (0.29), residues: 354 sheet: -0.66 (0.76), residues: 41 loop : -2.41 (0.30), residues: 361 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 0.009 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG A 460 *********************** 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 92 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 63 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8522 (tmm) cc_final: 0.8191 (tmm) REVERT: A 416 LYS cc_start: 0.8302 (tppt) cc_final: 0.7430 (tptt) REVERT: A 480 MET cc_start: 0.8809 (mtp) cc_final: 0.8587 (mtm) REVERT: A 489 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7094 (pm20) REVERT: E 423 TYR cc_start: 0.8183 (t80) cc_final: 0.7695 (t80) REVERT: E 471 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6905 (mm-30) outliers start: 29 outliers final: 24 residues processed: 85 average time/residue: 0.1706 time to fit residues: 21.0034 Evaluate side-chains 87 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 62 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.8620 ------------------------------------------------------------------------------- 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: 0.7908 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6599 Z= 0.209 Angle : 0.535 9.448 8960 Z= 0.265 Chirality : 0.045 0.290 966 Planarity : 0.003 0.035 1143 Dihedral : 6.237 57.072 1112 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.61 % Allowed : 21.28 % Favored : 74.11 % 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: -0.72 (0.31), residues: 756 helix: 1.21 (0.29), residues: 354 sheet: -0.61 (0.77), residues: 41 loop : -2.32 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.011 0.001 TYR A 183 ARG 0.001 0.000 ARG A 460 *********************** 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 93 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 62 time to evaluate : 1.288 Fit side-chains REVERT: A 190 MET cc_start: 0.8523 (tmm) cc_final: 0.8183 (tmm) REVERT: A 383 MET cc_start: 0.8784 (mtp) cc_final: 0.8399 (mtm) REVERT: A 416 LYS cc_start: 0.8316 (tppt) cc_final: 0.7436 (tptt) REVERT: A 480 MET cc_start: 0.8791 (mtp) cc_final: 0.8557 (mtm) REVERT: A 489 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: E 423 TYR cc_start: 0.8146 (t80) cc_final: 0.7646 (t80) outliers start: 31 outliers final: 24 residues processed: 86 average time/residue: 0.1701 time to fit residues: 21.4923 Evaluate side-chains 86 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6599 Z= 0.176 Angle : 0.523 9.437 8960 Z= 0.258 Chirality : 0.045 0.362 966 Planarity : 0.003 0.037 1143 Dihedral : 6.185 57.423 1112 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.76 % Allowed : 20.68 % Favored : 74.55 % 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: -0.58 (0.31), residues: 756 helix: 1.32 (0.29), residues: 354 sheet: -0.56 (0.78), residues: 41 loop : -2.23 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 315 TYR 0.009 0.001 TYR A 183 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 97 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 65 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7319 (mtt) cc_final: 0.6990 (mtt) REVERT: A 190 MET cc_start: 0.8527 (tmm) cc_final: 0.8176 (tmm) REVERT: A 416 LYS cc_start: 0.8278 (tppt) cc_final: 0.7405 (tptt) REVERT: A 480 MET cc_start: 0.8795 (mtp) cc_final: 0.8571 (mtm) REVERT: A 489 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7078 (pm20) REVERT: E 423 TYR cc_start: 0.8140 (t80) cc_final: 0.7634 (t80) outliers start: 32 outliers final: 27 residues processed: 90 average time/residue: 0.1403 time to fit residues: 18.4543 Evaluate side-chains 90 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 62 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER 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: 0.7980 chunk 45 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.0170 chunk 69 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4234 ------------------------------------------------------------------------------- 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: 0.7864 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6599 Z= 0.133 Angle : 0.499 9.438 8960 Z= 0.246 Chirality : 0.044 0.340 966 Planarity : 0.004 0.079 1143 Dihedral : 5.955 57.809 1112 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 4.17 % Allowed : 21.88 % Favored : 73.96 % 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: -0.50 (0.31), residues: 756 helix: 1.45 (0.29), residues: 356 sheet: -0.57 (0.79), residues: 41 loop : -2.29 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.002 0.001 HIS A 374 PHE 0.010 0.001 PHE A 315 TYR 0.008 0.001 TYR A 385 ARG 0.001 0.000 ARG E 357 *********************** 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 100 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7284 (mtt) cc_final: 0.6929 (mtt) REVERT: A 190 MET cc_start: 0.8526 (tmm) cc_final: 0.8192 (tmm) REVERT: A 416 LYS cc_start: 0.8229 (tppt) cc_final: 0.7388 (tptt) REVERT: A 480 MET cc_start: 0.8814 (mtp) cc_final: 0.8613 (mtm) REVERT: A 489 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7081 (pm20) REVERT: E 423 TYR cc_start: 0.8150 (t80) cc_final: 0.7642 (t80) outliers start: 28 outliers final: 23 residues processed: 93 average time/residue: 0.1519 time to fit residues: 20.5216 Evaluate side-chains 90 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6599 Z= 0.320 Angle : 0.612 13.423 8960 Z= 0.306 Chirality : 0.050 0.337 966 Planarity : 0.004 0.072 1143 Dihedral : 6.165 56.279 1109 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.72 % Allowed : 22.47 % Favored : 73.81 % 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: -0.58 (0.31), residues: 756 helix: 1.23 (0.29), residues: 360 sheet: -0.66 (0.78), residues: 41 loop : -2.17 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 PHE 0.013 0.001 PHE A 327 TYR 0.016 0.001 TYR A 183 ARG 0.002 0.000 ARG A 245 *********************** 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 88 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 63 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7260 (mtt) cc_final: 0.6942 (mtt) REVERT: A 190 MET cc_start: 0.8501 (tmm) cc_final: 0.8096 (tmm) REVERT: A 383 MET cc_start: 0.8823 (mtp) cc_final: 0.8597 (ttm) REVERT: A 416 LYS cc_start: 0.8330 (tppt) cc_final: 0.7416 (tptt) REVERT: A 480 MET cc_start: 0.8776 (mtp) cc_final: 0.8509 (mtm) REVERT: A 489 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: E 423 TYR cc_start: 0.8111 (t80) cc_final: 0.7722 (t80) outliers start: 25 outliers final: 21 residues processed: 83 average time/residue: 0.1520 time to fit residues: 18.6001 Evaluate side-chains 83 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6599 Z= 0.195 Angle : 0.560 11.293 8960 Z= 0.279 Chirality : 0.046 0.328 966 Planarity : 0.004 0.067 1143 Dihedral : 6.107 57.388 1109 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.27 % Allowed : 22.77 % Favored : 73.96 % 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: 1.36 (0.29), residues: 354 sheet: -0.64 (0.79), residues: 41 loop : -2.06 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 478 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 327 TYR 0.010 0.001 TYR A 183 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 87 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 65 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7239 (mtt) cc_final: 0.6893 (mtt) REVERT: A 190 MET cc_start: 0.8512 (tmm) cc_final: 0.8145 (tmm) REVERT: A 416 LYS cc_start: 0.8288 (tppt) cc_final: 0.7421 (tptt) REVERT: A 480 MET cc_start: 0.8801 (mtp) cc_final: 0.8557 (mtm) REVERT: A 489 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.7095 (pm20) REVERT: E 423 TYR cc_start: 0.8152 (t80) cc_final: 0.7705 (t80) outliers start: 22 outliers final: 21 residues processed: 82 average time/residue: 0.1440 time to fit residues: 17.3232 Evaluate side-chains 83 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 61 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 489 GLU Chi-restraints excluded: chain A residue 578 ASN Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 398 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 458 LYS Chi-restraints excluded: chain E residue 470 THR Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 500 THR Chi-restraints excluded: chain E residue 514 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.3980 chunk 59 optimal weight: 0.0010 chunk 24 optimal weight: 0.0870 chunk 61 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.2564 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.124894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.094779 restraints weight = 8950.208| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.44 r_work: 0.2737 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6599 Z= 0.124 Angle : 0.533 12.546 8960 Z= 0.258 Chirality : 0.044 0.315 966 Planarity : 0.004 0.060 1143 Dihedral : 5.725 58.165 1109 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.53 % Allowed : 23.96 % Favored : 73.51 % 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: -0.33 (0.32), residues: 756 helix: 1.48 (0.29), residues: 359 sheet: -0.61 (0.81), residues: 41 loop : -2.07 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A 417 PHE 0.011 0.001 PHE A 315 TYR 0.009 0.001 TYR E 380 ARG 0.002 0.000 ARG E 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.16 seconds wall clock time: 33 minutes 23.91 seconds (2003.91 seconds total)