Starting phenix.real_space_refine on Sat Apr 6 00:37:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9h_35272/04_2024/8i9h_35272.pdb" } resolution = 3.6 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 37 5.16 5 C 4161 2.51 5 N 1063 2.21 5 O 1253 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 GLU 23": "OE1" <-> "OE2" Residue "A GLU 37": "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 GLU 182": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" 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 GLU 329": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E GLU 471": "OE1" <-> "OE2" Residue "E GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6514 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: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 11, 'TRANS': 171} Chain breaks: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.95, per 1000 atoms: 0.61 Number of scatterers: 6514 At special positions: 0 Unit cell: (105.439, 86.96, 109.787, 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 37 16.00 O 1253 8.00 N 1063 7.00 C 4161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, 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=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 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: 2.50 Conformation dependent library (CDL) restraints added in 1.2 seconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 5 sheets defined 50.1% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.885A pdb=" N LYS A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 4.038A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.854A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.917A 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 102 removed outlier: 3.829A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.558A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 155 removed outlier: 3.789A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 171 removed outlier: 3.800A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 193 removed outlier: 4.571A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.552A pdb=" N TYR A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 4.317A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 removed outlier: 4.422A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 305 through 319 removed outlier: 3.778A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 4.025A pdb=" N ASN A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 385 removed outlier: 4.040A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.554A pdb=" N LEU A 392 " --> pdb=" O PRO A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.801A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.690A pdb=" N SER A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLY A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 444 removed outlier: 3.603A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 465 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: 4.099A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN A 531 " --> pdb=" O GLU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.526A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.709A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 559 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 581 through 596 removed outlier: 3.558A 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 337 through 341 removed outlier: 3.702A pdb=" N GLU E 340 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 364 through 368 removed outlier: 4.094A pdb=" N VAL E 367 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 403 through 410 removed outlier: 3.842A pdb=" N GLU E 406 " --> pdb=" O ARG E 403 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.570A pdb=" N ASP E 442 " --> pdb=" O SER E 438 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 438 through 443' Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.323A 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: 3.704A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.461A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE E 434 " --> pdb=" O VAL E 511 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.684A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 243 hydrogen bonds defined for protein. 666 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: 1.76 Time building geometry restraints manager: 2.73 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: 2061 1.34 - 1.46: 1712 1.46 - 1.58: 2864 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6695 Sorted by residual: bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" CA ASN A 149 " pdb=" C ASN A 149 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.41e-02 5.03e+03 3.54e+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 2.43e+00 bond pdb=" CA HIS E 339 " pdb=" C HIS E 339 " ideal model delta sigma weight residual 1.522 1.496 0.025 1.72e-02 3.38e+03 2.18e+00 ... (remaining 6690 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.07: 150 106.07 - 113.07: 3515 113.07 - 120.06: 2596 120.06 - 127.05: 2735 127.05 - 134.04: 101 Bond angle restraints: 9097 Sorted by residual: angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" C ILE A 21 " ideal model delta sigma weight residual 112.29 107.52 4.77 9.40e-01 1.13e+00 2.57e+01 angle pdb=" N GLU A 197 " pdb=" CA GLU A 197 " pdb=" CB GLU A 197 " ideal model delta sigma weight residual 114.17 109.20 4.97 1.14e+00 7.69e-01 1.90e+01 angle pdb=" CA PRO A 138 " pdb=" C PRO A 138 " pdb=" N GLN A 139 " ideal model delta sigma weight residual 116.45 119.77 -3.32 8.50e-01 1.38e+00 1.52e+01 angle pdb=" CA PRO A 138 " pdb=" C PRO A 138 " pdb=" O PRO A 138 " ideal model delta sigma weight residual 121.38 118.61 2.77 7.70e-01 1.69e+00 1.30e+01 angle pdb=" N ASP A 509 " pdb=" CA ASP A 509 " pdb=" C ASP A 509 " ideal model delta sigma weight residual 111.52 116.55 -5.03 1.40e+00 5.10e-01 1.29e+01 ... (remaining 9092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3526 17.99 - 35.98: 434 35.98 - 53.97: 130 53.97 - 71.95: 19 71.95 - 89.94: 7 Dihedral angle restraints: 4116 sinusoidal: 1824 harmonic: 2292 Sorted by residual: dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 60.27 32.73 1 1.00e+01 1.00e-02 1.52e+01 dihedral pdb=" CA GLY A 337 " pdb=" C GLY A 337 " pdb=" N ASN A 338 " pdb=" CA ASN A 338 " ideal model delta harmonic sigma weight residual -180.00 -160.64 -19.36 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 4113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 889 0.079 - 0.158: 92 0.158 - 0.237: 3 0.237 - 0.316: 1 0.316 - 0.395: 1 Chirality restraints: 986 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 -2.01 -0.39 2.00e-01 2.50e+01 3.89e+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 -2.25 -0.28 2.00e-01 2.50e+01 1.91e+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 -2.30 -0.20 2.00e-01 2.50e+01 9.66e-01 ... (remaining 983 not shown) Planarity restraints: 1168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 372 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO E 373 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 373 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 373 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " -0.028 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO E 463 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 582 " -0.026 5.00e-02 4.00e+02 3.86e-02 2.39e+00 pdb=" N PRO A 583 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.022 5.00e-02 4.00e+02 ... (remaining 1165 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 184 2.69 - 3.24: 6348 3.24 - 3.79: 9469 3.79 - 4.35: 11957 4.35 - 4.90: 20385 Nonbonded interactions: 48343 Sorted by model distance: nonbonded pdb=" N ASP A 111 " pdb=" OD1 ASP A 111 " model vdw 2.135 2.520 nonbonded pdb=" O ASN E 439 " pdb=" OG SER E 443 " model vdw 2.235 2.440 nonbonded pdb=" OG SER E 349 " pdb=" O LEU E 452 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASP A 382 " pdb=" OH TYR A 385 " model vdw 2.276 2.440 nonbonded pdb=" NH2 ARG E 357 " pdb=" O ILE E 358 " model vdw 2.277 2.520 ... (remaining 48338 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 group one per residue 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: 1.330 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: 0.020 Extract box with map and model: 5.240 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 21.220 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 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 : 0.006 0.056 6695 Z= 0.415 Angle : 0.708 6.601 9097 Z= 0.391 Chirality : 0.050 0.395 986 Planarity : 0.004 0.044 1161 Dihedral : 16.884 89.943 2626 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 7.58 % Allowed : 19.24 % Favored : 73.18 % 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: -4.33 (0.24), residues: 774 helix: -2.10 (0.23), residues: 359 sheet: -2.11 (0.64), residues: 48 loop : -3.87 (0.24), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 436 HIS 0.003 0.001 HIS A 241 PHE 0.012 0.002 PHE E 400 TYR 0.017 0.001 TYR A 183 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 87 time to evaluate : 0.714 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.8873 (tmtt) cc_final: 0.8352 (tptp) REVERT: A 115 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7492 (tpt170) REVERT: A 154 ASN cc_start: 0.8106 (m-40) cc_final: 0.7866 (t0) REVERT: A 156 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8576 (tt) REVERT: A 224 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: A 367 ASP cc_start: 0.6928 (p0) cc_final: 0.6700 (p0) REVERT: E 414 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9015 (tp40) REVERT: E 466 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7425 (ptm160) outliers start: 52 outliers final: 41 residues processed: 134 average time/residue: 0.1898 time to fit residues: 33.9370 Evaluate side-chains 120 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 76 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 432 ASN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 494 SER Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.0570 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 23 optimal weight: 0.0570 chunk 36 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 0.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 102 GLN A 239 HIS A 340 GLN A 374 HIS A 378 HIS A 472 GLN A 505 HIS A 522 GLN A 535 HIS A 599 ASN ** E 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6695 Z= 0.156 Angle : 0.604 15.531 9097 Z= 0.288 Chirality : 0.044 0.286 986 Planarity : 0.004 0.058 1161 Dihedral : 9.499 58.865 1192 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 5.10 % Allowed : 22.16 % Favored : 72.74 % 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: -2.97 (0.27), residues: 774 helix: -0.86 (0.28), residues: 360 sheet: -1.43 (0.69), residues: 48 loop : -3.31 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 163 HIS 0.004 0.001 HIS A 265 PHE 0.012 0.001 PHE A 428 TYR 0.011 0.001 TYR A 183 ARG 0.002 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 83 time to evaluate : 0.803 Fit side-chains REVERT: A 31 LYS cc_start: 0.8770 (tmtt) cc_final: 0.8280 (tptp) REVERT: A 33 ASN cc_start: 0.9106 (m-40) cc_final: 0.8886 (t0) REVERT: A 82 MET cc_start: 0.7878 (ttp) cc_final: 0.6983 (tmm) REVERT: A 101 GLN cc_start: 0.8930 (tt0) cc_final: 0.8651 (tt0) REVERT: A 340 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7485 (mm110) REVERT: A 363 LYS cc_start: 0.7992 (pttp) cc_final: 0.7617 (pttm) REVERT: A 406 GLU cc_start: 0.8261 (tp30) cc_final: 0.8054 (tp30) REVERT: A 474 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8324 (mmm) REVERT: E 414 GLN cc_start: 0.9257 (mm-40) cc_final: 0.9007 (tp40) outliers start: 35 outliers final: 20 residues processed: 109 average time/residue: 0.1553 time to fit residues: 23.9791 Evaluate side-chains 104 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 468 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 47 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.0060 chunk 56 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 GLN A 437 ASN E 339 HIS E 409 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6695 Z= 0.196 Angle : 0.570 12.198 9097 Z= 0.275 Chirality : 0.044 0.299 986 Planarity : 0.004 0.057 1161 Dihedral : 7.859 59.110 1142 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.96 % Allowed : 23.18 % Favored : 71.87 % 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: -2.47 (0.29), residues: 774 helix: -0.41 (0.28), residues: 365 sheet: -1.29 (0.70), residues: 48 loop : -3.09 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.003 0.001 HIS A 535 PHE 0.011 0.001 PHE A 428 TYR 0.011 0.001 TYR A 183 ARG 0.001 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 83 time to evaluate : 0.732 Fit side-chains REVERT: A 31 LYS cc_start: 0.8753 (tmtt) cc_final: 0.8231 (tptp) REVERT: A 33 ASN cc_start: 0.9106 (m-40) cc_final: 0.8862 (t0) REVERT: A 82 MET cc_start: 0.7891 (ttp) cc_final: 0.6993 (tmm) REVERT: A 101 GLN cc_start: 0.8894 (tt0) cc_final: 0.8621 (tt0) REVERT: A 249 MET cc_start: 0.8175 (ttp) cc_final: 0.7859 (tmm) REVERT: A 256 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8736 (mm) REVERT: A 306 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.6883 (tpp-160) REVERT: A 323 MET cc_start: 0.8229 (mmm) cc_final: 0.7876 (mmm) REVERT: A 479 GLU cc_start: 0.8385 (tp30) cc_final: 0.8139 (tp30) REVERT: E 414 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8999 (tp40) REVERT: E 471 GLU cc_start: 0.8617 (mp0) cc_final: 0.8104 (mp0) outliers start: 34 outliers final: 23 residues processed: 111 average time/residue: 0.1509 time to fit residues: 24.1421 Evaluate side-chains 106 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6695 Z= 0.277 Angle : 0.620 20.358 9097 Z= 0.290 Chirality : 0.046 0.296 986 Planarity : 0.004 0.056 1161 Dihedral : 7.625 58.985 1140 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.96 % Allowed : 23.76 % Favored : 71.28 % 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: -2.25 (0.29), residues: 774 helix: -0.22 (0.29), residues: 365 sheet: -1.17 (0.71), residues: 48 loop : -3.00 (0.27), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 436 HIS 0.002 0.001 HIS A 241 PHE 0.012 0.001 PHE A 327 TYR 0.013 0.001 TYR A 183 ARG 0.001 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 0.783 Fit side-chains REVERT: A 31 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8211 (tptp) REVERT: A 82 MET cc_start: 0.7895 (ttp) cc_final: 0.6929 (tmm) REVERT: A 101 GLN cc_start: 0.8892 (tt0) cc_final: 0.8602 (tt0) REVERT: A 249 MET cc_start: 0.8147 (ttp) cc_final: 0.7822 (tmm) REVERT: A 256 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8759 (mm) REVERT: A 306 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6972 (tpp-160) REVERT: A 479 GLU cc_start: 0.8469 (tp30) cc_final: 0.8156 (tp30) REVERT: E 414 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8982 (tp40) REVERT: E 471 GLU cc_start: 0.8653 (mp0) cc_final: 0.8347 (mp0) outliers start: 34 outliers final: 23 residues processed: 110 average time/residue: 0.1672 time to fit residues: 25.8782 Evaluate side-chains 102 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 77 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP 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 142 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 418 ILE Chi-restraints excluded: chain E residue 422 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6695 Z= 0.175 Angle : 0.587 20.949 9097 Z= 0.271 Chirality : 0.044 0.297 986 Planarity : 0.004 0.055 1161 Dihedral : 7.294 58.970 1140 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.66 % Allowed : 25.22 % Favored : 70.12 % 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: -1.92 (0.29), residues: 774 helix: 0.05 (0.29), residues: 362 sheet: -0.92 (0.72), residues: 48 loop : -2.80 (0.28), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.011 0.001 PHE E 342 TYR 0.011 0.001 TYR A 183 ARG 0.001 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 86 time to evaluate : 0.675 Fit side-chains REVERT: A 31 LYS cc_start: 0.8675 (tmtt) cc_final: 0.8146 (tptp) REVERT: A 82 MET cc_start: 0.7954 (ttp) cc_final: 0.6957 (tmm) REVERT: A 101 GLN cc_start: 0.8840 (tt0) cc_final: 0.8558 (tt0) REVERT: A 249 MET cc_start: 0.8095 (ttp) cc_final: 0.7826 (tmm) REVERT: A 256 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8765 (mm) REVERT: A 306 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7260 (tpp-160) REVERT: A 479 GLU cc_start: 0.8403 (tp30) cc_final: 0.8104 (tp30) REVERT: A 495 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7959 (mm-30) REVERT: A 557 MET cc_start: 0.8957 (tmm) cc_final: 0.8664 (tmm) REVERT: E 414 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8964 (tp40) REVERT: E 428 ASP cc_start: 0.8149 (p0) cc_final: 0.7836 (t0) REVERT: E 471 GLU cc_start: 0.8632 (mp0) cc_final: 0.8338 (mp0) outliers start: 32 outliers final: 22 residues processed: 110 average time/residue: 0.1458 time to fit residues: 22.9769 Evaluate side-chains 107 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 83 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN E 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6695 Z= 0.221 Angle : 0.604 20.106 9097 Z= 0.282 Chirality : 0.045 0.295 986 Planarity : 0.004 0.055 1161 Dihedral : 7.122 58.530 1140 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.23 % Allowed : 24.78 % Favored : 70.99 % 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: -1.65 (0.30), residues: 774 helix: 0.26 (0.30), residues: 354 sheet: -0.78 (0.72), residues: 48 loop : -2.60 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 0.001 HIS A 241 PHE 0.011 0.001 PHE E 342 TYR 0.012 0.001 TYR A 183 ARG 0.002 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.706 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7960 (ttp) cc_final: 0.6925 (tmm) REVERT: A 101 GLN cc_start: 0.8830 (tt0) cc_final: 0.8539 (tt0) REVERT: A 249 MET cc_start: 0.7980 (ttp) cc_final: 0.7699 (tmm) REVERT: A 256 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8762 (mm) REVERT: A 479 GLU cc_start: 0.8496 (tp30) cc_final: 0.8166 (tp30) REVERT: A 495 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7937 (mm-30) REVERT: A 557 MET cc_start: 0.8935 (tmm) cc_final: 0.8602 (tmm) REVERT: E 414 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8897 (tp40) REVERT: E 428 ASP cc_start: 0.8137 (p0) cc_final: 0.7905 (t0) REVERT: E 466 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7805 (ptm160) REVERT: E 471 GLU cc_start: 0.8648 (mp0) cc_final: 0.8346 (mp0) outliers start: 29 outliers final: 21 residues processed: 105 average time/residue: 0.1435 time to fit residues: 21.5810 Evaluate side-chains 104 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 62 optimal weight: 0.0170 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6695 Z= 0.157 Angle : 0.629 27.800 9097 Z= 0.274 Chirality : 0.047 0.503 986 Planarity : 0.004 0.054 1161 Dihedral : 7.452 58.639 1135 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.23 % Allowed : 24.93 % Favored : 70.85 % 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: -1.55 (0.30), residues: 774 helix: 0.31 (0.29), residues: 360 sheet: -0.65 (0.73), residues: 48 loop : -2.56 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.002 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 582 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 83 time to evaluate : 0.764 Fit side-chains REVERT: A 31 LYS cc_start: 0.8606 (tmtt) cc_final: 0.8313 (tppt) REVERT: A 82 MET cc_start: 0.7897 (ttp) cc_final: 0.6902 (tmm) REVERT: A 101 GLN cc_start: 0.8781 (tt0) cc_final: 0.8518 (tt0) REVERT: A 249 MET cc_start: 0.8088 (ttp) cc_final: 0.7826 (tmm) REVERT: A 256 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8767 (mm) REVERT: A 479 GLU cc_start: 0.8422 (tp30) cc_final: 0.8125 (tp30) REVERT: A 495 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7886 (mm-30) REVERT: A 557 MET cc_start: 0.8920 (tmm) cc_final: 0.8577 (tmm) REVERT: E 414 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8909 (tp40) REVERT: E 466 ARG cc_start: 0.8172 (ptm160) cc_final: 0.7842 (ptm160) REVERT: E 471 GLU cc_start: 0.8638 (mp0) cc_final: 0.8403 (mp0) outliers start: 29 outliers final: 23 residues processed: 106 average time/residue: 0.1517 time to fit residues: 23.5589 Evaluate side-chains 108 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 67 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6695 Z= 0.164 Angle : 0.645 30.344 9097 Z= 0.276 Chirality : 0.045 0.297 986 Planarity : 0.004 0.054 1161 Dihedral : 7.738 72.445 1135 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.08 % Allowed : 25.36 % Favored : 70.55 % 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: -1.41 (0.30), residues: 774 helix: 0.46 (0.29), residues: 360 sheet: -0.57 (0.73), residues: 48 loop : -2.52 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 436 HIS 0.005 0.001 HIS E 339 PHE 0.009 0.001 PHE A 327 TYR 0.010 0.001 TYR A 183 ARG 0.001 0.000 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 0.777 Fit side-chains REVERT: A 31 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8266 (tppt) REVERT: A 82 MET cc_start: 0.7908 (ttp) cc_final: 0.6868 (tmm) REVERT: A 101 GLN cc_start: 0.8750 (tt0) cc_final: 0.8481 (tt0) REVERT: A 171 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 249 MET cc_start: 0.8080 (ttp) cc_final: 0.7818 (tmm) REVERT: A 479 GLU cc_start: 0.8472 (tp30) cc_final: 0.8119 (tp30) REVERT: A 495 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7827 (mm-30) REVERT: A 557 MET cc_start: 0.8912 (tmm) cc_final: 0.8567 (tmm) REVERT: E 466 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7889 (ptm160) REVERT: E 471 GLU cc_start: 0.8633 (mp0) cc_final: 0.8393 (mp0) outliers start: 28 outliers final: 24 residues processed: 110 average time/residue: 0.1591 time to fit residues: 25.1754 Evaluate side-chains 112 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 65 optimal weight: 0.0870 chunk 68 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6695 Z= 0.135 Angle : 0.620 29.823 9097 Z= 0.270 Chirality : 0.042 0.294 986 Planarity : 0.004 0.053 1161 Dihedral : 6.070 58.718 1132 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.06 % Allowed : 26.38 % Favored : 70.55 % 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: -1.20 (0.30), residues: 774 helix: 0.64 (0.29), residues: 359 sheet: -0.44 (0.74), residues: 48 loop : -2.42 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.002 0.001 HIS A 265 PHE 0.007 0.001 PHE A 327 TYR 0.009 0.001 TYR A 385 ARG 0.002 0.000 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.679 Fit side-chains REVERT: A 31 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8285 (tppt) REVERT: A 82 MET cc_start: 0.7905 (ttp) cc_final: 0.6867 (tmm) REVERT: A 101 GLN cc_start: 0.8672 (tt0) cc_final: 0.8405 (tt0) REVERT: A 479 GLU cc_start: 0.8391 (tp30) cc_final: 0.8070 (tp30) REVERT: A 557 MET cc_start: 0.8943 (tmm) cc_final: 0.8588 (tmm) REVERT: E 406 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8562 (tt0) REVERT: E 417 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7148 (t0) REVERT: E 471 GLU cc_start: 0.8612 (mp0) cc_final: 0.8381 (mp0) outliers start: 21 outliers final: 16 residues processed: 104 average time/residue: 0.1365 time to fit residues: 20.7288 Evaluate side-chains 102 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 47 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 409 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6695 Z= 0.147 Angle : 0.636 31.404 9097 Z= 0.274 Chirality : 0.043 0.291 986 Planarity : 0.004 0.053 1161 Dihedral : 5.915 58.892 1130 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.06 % Allowed : 25.51 % Favored : 71.43 % 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: -1.11 (0.30), residues: 774 helix: 0.72 (0.29), residues: 365 sheet: -0.31 (0.76), residues: 48 loop : -2.45 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 417 PHE 0.008 0.001 PHE A 327 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG E 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 86 time to evaluate : 0.735 Fit side-chains REVERT: A 31 LYS cc_start: 0.8510 (tmtt) cc_final: 0.8246 (tppt) REVERT: A 82 MET cc_start: 0.7909 (ttp) cc_final: 0.6875 (tmm) REVERT: A 101 GLN cc_start: 0.8660 (tt0) cc_final: 0.8432 (tt0) REVERT: A 156 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8509 (tt) REVERT: A 278 LEU cc_start: 0.9121 (mt) cc_final: 0.8777 (mt) REVERT: A 479 GLU cc_start: 0.8447 (tp30) cc_final: 0.8114 (tp30) REVERT: A 557 MET cc_start: 0.8938 (tmm) cc_final: 0.8579 (tmm) REVERT: E 339 HIS cc_start: 0.8303 (m-70) cc_final: 0.8082 (m170) REVERT: E 417 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7178 (t0) REVERT: E 465 GLU cc_start: 0.9039 (tp30) cc_final: 0.8830 (tp30) REVERT: E 471 GLU cc_start: 0.8615 (mp0) cc_final: 0.8379 (mp0) outliers start: 21 outliers final: 19 residues processed: 102 average time/residue: 0.1466 time to fit residues: 22.1978 Evaluate side-chains 106 residues out of total 686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 369 TYR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 383 SER Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 477 ASN Chi-restraints excluded: chain E residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.0870 chunk 25 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 GLN E 409 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.111369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093036 restraints weight = 11224.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096320 restraints weight = 5667.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098567 restraints weight = 3540.304| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6695 Z= 0.145 Angle : 0.629 30.789 9097 Z= 0.275 Chirality : 0.043 0.291 986 Planarity : 0.004 0.052 1161 Dihedral : 5.793 58.903 1130 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.35 % Allowed : 25.36 % Favored : 71.28 % 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: -0.97 (0.30), residues: 774 helix: 0.85 (0.29), residues: 365 sheet: -0.24 (0.77), residues: 48 loop : -2.38 (0.29), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 436 HIS 0.004 0.001 HIS A 417 PHE 0.008 0.001 PHE A 327 TYR 0.009 0.001 TYR A 183 ARG 0.001 0.000 ARG E 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.28 seconds wall clock time: 31 minutes 14.82 seconds (1874.82 seconds total)