Starting phenix.real_space_refine on Fri Jul 19 04:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9g_35270/07_2024/8i9g_35270.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9g_35270/07_2024/8i9g_35270.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/8i9g_35270/07_2024/8i9g_35270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9g_35270/07_2024/8i9g_35270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9g_35270/07_2024/8i9g_35270.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9g_35270/07_2024/8i9g_35270.cif" } 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= 0.003 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 36 5.16 5 C 4159 2.51 5 N 1061 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 140": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 430": "OE1" <-> "OE2" Residue "D GLU 435": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D GLU 549": "OE1" <-> "OE2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 516": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6507 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" 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: "A" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1455 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} 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: "E" 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: "D" 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: 4.31, per 1000 atoms: 0.66 Number of scatterers: 6507 At special positions: 0 Unit cell: (104.352, 90.221, 107.613, 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 36 16.00 O 1251 8.00 N 1061 7.00 C 4159 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 1 " - " ASN D 53 " " NAG C 1 " - " ASN D 90 " " NAG D 701 " - " ASN D 322 " " NAG E 1 " - " ASN D 103 " " NAG F 1 " - " ASN D 432 " " NAG G 1 " - " ASN D 546 " " NAG H 1 " - " ASN A 343 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.1 seconds 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 51.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.776A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.797A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.893A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.944A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.779A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 193 removed outlier: 3.909A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.640A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 230 removed outlier: 4.122A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.833A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.728A pdb=" N TYR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 300 Processing helix chain 'D' and resid 305 through 318 removed outlier: 3.858A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.857A pdb=" N ASN D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER D 331 " --> pdb=" O PHE D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.070A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.692A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.877A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.913A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.631A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 4.162A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN D 531 " --> pdb=" O GLU D 527 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 532 " --> pdb=" O ALA D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.608A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.897A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 581 through 599 removed outlier: 3.532A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.380A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.699A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.976A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.921A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.243A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.655A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 259 hydrogen bonds defined for protein. 735 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: 1.53 Time building geometry restraints manager: 2.82 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: 2058 1.34 - 1.47: 1773 1.47 - 1.59: 2798 1.59 - 1.71: 0 1.71 - 1.84: 57 Bond restraints: 6686 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.84e+00 bond pdb=" C ALA A 372 " pdb=" N PRO A 373 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.38e-02 5.25e+03 2.82e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" C VAL A 382 " pdb=" N SER A 383 " ideal model delta sigma weight residual 1.329 1.354 -0.025 1.60e-02 3.91e+03 2.47e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 ... (remaining 6681 not shown) Histogram of bond angle deviations from ideal: 99.42 - 106.34: 199 106.34 - 113.26: 3499 113.26 - 120.18: 2598 120.18 - 127.10: 2690 127.10 - 134.02: 97 Bond angle restraints: 9083 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 115.61 108.41 7.20 1.74e+00 3.30e-01 1.71e+01 angle pdb=" N ARG A 452 " pdb=" CA ARG A 452 " pdb=" C ARG A 452 " ideal model delta sigma weight residual 110.44 114.92 -4.48 1.20e+00 6.94e-01 1.39e+01 angle pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta sigma weight residual 123.96 119.34 4.62 1.44e+00 4.82e-01 1.03e+01 angle pdb=" C GLN A 493 " pdb=" N SER A 494 " pdb=" CA SER A 494 " ideal model delta sigma weight residual 121.31 125.48 -4.17 1.49e+00 4.50e-01 7.85e+00 angle pdb=" N GLY D 337 " pdb=" CA GLY D 337 " pdb=" C GLY D 337 " ideal model delta sigma weight residual 113.18 119.63 -6.45 2.37e+00 1.78e-01 7.42e+00 ... (remaining 9078 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 3531 17.70 - 35.40: 426 35.40 - 53.10: 108 53.10 - 70.79: 31 70.79 - 88.49: 6 Dihedral angle restraints: 4102 sinusoidal: 1819 harmonic: 2283 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -15.34 -70.66 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CA TYR A 451 " pdb=" C TYR A 451 " pdb=" N ARG A 452 " pdb=" CA ARG A 452 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" N ALA A 372 " pdb=" CA ALA A 372 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 4099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 668 0.043 - 0.086: 243 0.086 - 0.129: 68 0.129 - 0.172: 2 0.172 - 0.215: 4 Chirality restraints: 985 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.71e+01 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.33 -0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 982 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.082 2.00e-02 2.50e+03 6.72e-02 5.64e+01 pdb=" C7 NAG H 2 " 0.022 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.035 2.00e-02 2.50e+03 3.84e-02 1.84e+01 pdb=" CG ASN A 343 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.061 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " -0.046 2.00e-02 2.50e+03 3.75e-02 1.76e+01 pdb=" C7 NAG H 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " 0.059 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.009 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1003 2.75 - 3.29: 5898 3.29 - 3.83: 9954 3.83 - 4.36: 11729 4.36 - 4.90: 20829 Nonbonded interactions: 49413 Sorted by model distance: nonbonded pdb=" O PHE A 392 " pdb=" OG1 THR A 523 " model vdw 2.213 2.440 nonbonded pdb=" NZ LYS D 288 " pdb=" OE1 GLU D 433 " model vdw 2.239 2.520 nonbonded pdb=" ND2 ASN D 134 " pdb=" OD1 ASP D 136 " model vdw 2.278 2.520 nonbonded pdb=" N ASP D 431 " pdb=" OD1 ASP D 431 " model vdw 2.347 2.520 nonbonded pdb=" OG SER A 438 " pdb=" OD2 ASP A 442 " model vdw 2.352 2.440 ... (remaining 49408 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 'E' 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 20.720 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.005 0.044 6686 Z= 0.306 Angle : 0.670 7.201 9083 Z= 0.372 Chirality : 0.046 0.215 985 Planarity : 0.005 0.067 1159 Dihedral : 16.413 88.492 2621 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 4.97 % Allowed : 16.23 % Favored : 78.80 % 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: -3.28 (0.26), residues: 770 helix: -1.15 (0.26), residues: 358 sheet: -2.17 (0.67), residues: 49 loop : -3.31 (0.25), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS D 241 PHE 0.012 0.001 PHE A 375 TYR 0.013 0.001 TYR D 183 ARG 0.003 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 75 time to evaluate : 0.762 Fit side-chains REVERT: D 86 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7680 (tm-30) REVERT: D 131 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8613 (mtmp) REVERT: D 140 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7231 (tm-30) REVERT: D 256 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8584 (mm) REVERT: D 332 MET cc_start: 0.8069 (ttp) cc_final: 0.7740 (ttm) REVERT: D 431 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7244 (p0) REVERT: D 522 GLN cc_start: 0.8445 (tt0) cc_final: 0.8227 (tt0) REVERT: A 420 ASP cc_start: 0.7387 (m-30) cc_final: 0.7168 (m-30) REVERT: A 467 ASP cc_start: 0.7523 (t0) cc_final: 0.6987 (t0) outliers start: 34 outliers final: 24 residues processed: 106 average time/residue: 0.1887 time to fit residues: 26.6068 Evaluate side-chains 87 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 409 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 GLN D 58 ASN D 96 GLN D 239 HIS D 277 ASN D 345 HIS D 378 HIS D 472 GLN D 493 HIS D 505 HIS D 522 GLN D 599 ASN A 354 ASN A 460 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6686 Z= 0.298 Angle : 0.610 9.305 9083 Z= 0.311 Chirality : 0.046 0.270 985 Planarity : 0.004 0.055 1159 Dihedral : 9.940 84.043 1165 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 5.41 % Allowed : 18.42 % Favored : 76.17 % 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: -2.32 (0.28), residues: 770 helix: -0.33 (0.27), residues: 369 sheet: -1.52 (0.73), residues: 49 loop : -2.96 (0.26), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE D 32 TYR 0.014 0.001 TYR D 183 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 63 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 131 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8645 (mtmp) REVERT: D 140 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7149 (tm-30) REVERT: D 256 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8558 (mm) REVERT: D 332 MET cc_start: 0.8214 (ttp) cc_final: 0.7759 (ttm) REVERT: D 366 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.7215 (tpp) REVERT: D 465 LYS cc_start: 0.8705 (tttt) cc_final: 0.8466 (tttm) REVERT: A 420 ASP cc_start: 0.7390 (m-30) cc_final: 0.7089 (m-30) REVERT: A 454 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7076 (ttm170) outliers start: 37 outliers final: 25 residues processed: 92 average time/residue: 0.1690 time to fit residues: 21.4006 Evaluate side-chains 88 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 59 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 256 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 47 optimal weight: 0.0010 chunk 19 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 345 HIS D 522 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6686 Z= 0.157 Angle : 0.542 9.420 9083 Z= 0.273 Chirality : 0.042 0.275 985 Planarity : 0.004 0.050 1159 Dihedral : 8.696 80.205 1148 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.39 % Allowed : 19.44 % Favored : 76.17 % 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: -1.64 (0.29), residues: 770 helix: 0.22 (0.28), residues: 362 sheet: -1.10 (0.73), residues: 49 loop : -2.54 (0.27), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.009 0.001 HIS D 345 PHE 0.010 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 63 time to evaluate : 0.643 Fit side-chains REVERT: D 86 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7611 (tm-30) REVERT: D 140 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7260 (pp20) REVERT: D 213 ASP cc_start: 0.8540 (t0) cc_final: 0.8332 (t0) REVERT: D 332 MET cc_start: 0.8150 (ttp) cc_final: 0.7805 (ttm) REVERT: D 366 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7064 (tpp) REVERT: A 420 ASP cc_start: 0.7323 (m-30) cc_final: 0.6952 (m-30) outliers start: 30 outliers final: 22 residues processed: 86 average time/residue: 0.1592 time to fit residues: 19.1483 Evaluate side-chains 80 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 57 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS D 522 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 6686 Z= 0.364 Angle : 0.620 9.214 9083 Z= 0.315 Chirality : 0.047 0.268 985 Planarity : 0.005 0.067 1159 Dihedral : 8.475 79.589 1142 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 5.99 % Allowed : 18.71 % Favored : 75.29 % 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: -1.34 (0.29), residues: 770 helix: 0.48 (0.28), residues: 353 sheet: -0.96 (0.76), residues: 49 loop : -2.34 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.013 0.001 PHE D 32 TYR 0.017 0.001 TYR D 183 ARG 0.002 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 60 time to evaluate : 0.768 Fit side-chains REVERT: D 86 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7591 (tm-30) REVERT: D 131 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8578 (mtmp) REVERT: D 140 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7161 (tm-30) REVERT: D 332 MET cc_start: 0.8163 (ttp) cc_final: 0.7807 (ttm) REVERT: D 366 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7129 (tpp) REVERT: A 420 ASP cc_start: 0.7403 (m-30) cc_final: 0.7088 (m-30) REVERT: A 454 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7150 (ttm170) outliers start: 41 outliers final: 32 residues processed: 92 average time/residue: 0.1679 time to fit residues: 21.5636 Evaluate side-chains 93 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 58 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 578 ASN Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6686 Z= 0.177 Angle : 0.544 9.312 9083 Z= 0.274 Chirality : 0.042 0.279 985 Planarity : 0.004 0.071 1159 Dihedral : 7.988 78.765 1141 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.24 % Allowed : 20.76 % 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: -1.05 (0.30), residues: 770 helix: 0.70 (0.28), residues: 358 sheet: -0.86 (0.75), residues: 49 loop : -2.19 (0.28), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 163 HIS 0.004 0.001 HIS D 345 PHE 0.010 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 0.000 ARG A 452 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 65 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7699 (tm-30) REVERT: D 134 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.6606 (m110) REVERT: D 145 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7351 (tp30) REVERT: D 332 MET cc_start: 0.8074 (ttp) cc_final: 0.7742 (ttm) REVERT: D 366 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6913 (tpp) REVERT: D 376 MET cc_start: 0.8110 (mmm) cc_final: 0.7735 (mmm) REVERT: D 465 LYS cc_start: 0.8661 (tttm) cc_final: 0.8447 (tttt) REVERT: A 420 ASP cc_start: 0.7359 (m-30) cc_final: 0.6947 (m-30) outliers start: 29 outliers final: 22 residues processed: 87 average time/residue: 0.1751 time to fit residues: 20.9841 Evaluate side-chains 85 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 61 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 483 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6686 Z= 0.196 Angle : 0.544 9.356 9083 Z= 0.274 Chirality : 0.043 0.276 985 Planarity : 0.004 0.058 1159 Dihedral : 7.625 76.560 1139 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.24 % Allowed : 20.76 % 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: -0.86 (0.30), residues: 770 helix: 0.88 (0.28), residues: 357 sheet: -0.75 (0.75), residues: 49 loop : -2.11 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 0.000 ARG D 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 66 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: D 86 GLN cc_start: 0.8267 (tm-30) cc_final: 0.7709 (tm-30) REVERT: D 134 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.6728 (m110) REVERT: D 332 MET cc_start: 0.8079 (ttp) cc_final: 0.7750 (ttm) REVERT: D 366 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6878 (tpp) REVERT: D 376 MET cc_start: 0.8146 (mmm) cc_final: 0.7793 (mmm) REVERT: A 420 ASP cc_start: 0.7352 (m-30) cc_final: 0.6869 (m-30) REVERT: A 454 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6995 (ttm170) REVERT: A 500 THR cc_start: 0.9196 (p) cc_final: 0.8858 (p) outliers start: 29 outliers final: 24 residues processed: 90 average time/residue: 0.1781 time to fit residues: 22.1433 Evaluate side-chains 87 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 131 LYS Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6686 Z= 0.189 Angle : 0.542 9.359 9083 Z= 0.273 Chirality : 0.043 0.278 985 Planarity : 0.004 0.073 1159 Dihedral : 7.503 74.151 1139 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 4.39 % Allowed : 21.49 % Favored : 74.12 % 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: -0.67 (0.30), residues: 770 helix: 1.02 (0.29), residues: 357 sheet: -0.65 (0.77), residues: 49 loop : -2.00 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS D 241 PHE 0.010 0.001 PHE D 32 TYR 0.010 0.001 TYR A 495 ARG 0.001 0.000 ARG D 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 64 time to evaluate : 0.742 Fit side-chains REVERT: D 86 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7698 (tm-30) REVERT: D 140 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7283 (tm-30) REVERT: D 145 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7187 (tp30) REVERT: D 332 MET cc_start: 0.8062 (ttp) cc_final: 0.7731 (ttm) REVERT: D 366 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6854 (tpp) REVERT: D 376 MET cc_start: 0.8168 (mmm) cc_final: 0.7826 (mmm) REVERT: D 401 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7375 (m90) REVERT: A 420 ASP cc_start: 0.7341 (m-30) cc_final: 0.6848 (m-30) REVERT: A 454 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7009 (ttm170) REVERT: A 500 THR cc_start: 0.9182 (p) cc_final: 0.8841 (p) outliers start: 30 outliers final: 23 residues processed: 88 average time/residue: 0.1930 time to fit residues: 22.7148 Evaluate side-chains 86 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 60 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 522 GLN Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL 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: 0.6980 chunk 47 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6686 Z= 0.163 Angle : 0.533 9.385 9083 Z= 0.267 Chirality : 0.042 0.280 985 Planarity : 0.004 0.060 1159 Dihedral : 6.992 70.767 1133 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.09 % Allowed : 21.49 % Favored : 74.42 % 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: -0.49 (0.30), residues: 770 helix: 1.14 (0.29), residues: 358 sheet: -0.40 (0.78), residues: 49 loop : -1.90 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.003 0.001 HIS D 241 PHE 0.009 0.001 PHE D 32 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1540 Ramachandran restraints generated. 770 Oldfield, 0 Emsley, 770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 61 time to evaluate : 0.745 Fit side-chains REVERT: D 86 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7681 (tm-30) REVERT: D 140 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7287 (tm-30) REVERT: D 142 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8158 (pp) REVERT: D 145 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7356 (tp30) REVERT: D 332 MET cc_start: 0.8066 (ttp) cc_final: 0.7716 (ttm) REVERT: D 366 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6803 (tpp) REVERT: D 376 MET cc_start: 0.8165 (mmm) cc_final: 0.7818 (mmm) REVERT: D 401 HIS cc_start: 0.8452 (OUTLIER) cc_final: 0.7339 (m90) REVERT: A 420 ASP cc_start: 0.7312 (m-30) cc_final: 0.6821 (m-30) REVERT: A 454 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.6938 (ttm170) REVERT: A 500 THR cc_start: 0.9138 (p) cc_final: 0.8794 (p) outliers start: 28 outliers final: 20 residues processed: 84 average time/residue: 0.1899 time to fit residues: 21.6218 Evaluate side-chains 83 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 59 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 111 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 247 LYS Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 523 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.2273 > 50: distance: 58 - 62: 21.424 distance: 62 - 63: 15.645 distance: 63 - 64: 19.691 distance: 63 - 66: 23.710 distance: 64 - 65: 12.316 distance: 64 - 70: 21.660 distance: 66 - 67: 44.707 distance: 66 - 68: 40.875 distance: 67 - 69: 12.103 distance: 70 - 71: 30.738 distance: 70 - 76: 24.343 distance: 71 - 72: 21.416 distance: 71 - 74: 14.571 distance: 72 - 73: 7.047 distance: 72 - 77: 28.872 distance: 74 - 75: 36.574 distance: 75 - 76: 35.354 distance: 77 - 78: 27.830 distance: 78 - 79: 17.859 distance: 78 - 81: 42.374 distance: 79 - 80: 34.958 distance: 79 - 86: 14.591 distance: 81 - 82: 25.508 distance: 82 - 83: 4.290 distance: 83 - 84: 25.807 distance: 84 - 85: 29.539 distance: 86 - 87: 28.992 distance: 87 - 88: 13.474 distance: 87 - 90: 22.254 distance: 88 - 89: 30.587 distance: 88 - 94: 35.024 distance: 90 - 91: 10.351 distance: 91 - 92: 7.628 distance: 91 - 93: 15.999 distance: 94 - 95: 9.771 distance: 95 - 96: 19.541 distance: 95 - 98: 15.677 distance: 96 - 97: 10.226 distance: 96 - 103: 18.754 distance: 97 - 134: 15.024 distance: 98 - 99: 13.964 distance: 99 - 100: 16.694 distance: 100 - 101: 29.061 distance: 100 - 102: 36.085 distance: 104 - 105: 14.290 distance: 104 - 107: 19.424 distance: 105 - 106: 5.717 distance: 106 - 143: 33.520 distance: 107 - 108: 18.815 distance: 108 - 109: 10.802 distance: 108 - 110: 10.351 distance: 109 - 111: 10.669 distance: 110 - 112: 7.049 distance: 111 - 112: 7.850 distance: 113 - 115: 3.270 distance: 114 - 116: 4.983 distance: 117 - 118: 24.182 distance: 118 - 119: 4.848 distance: 118 - 121: 12.494 distance: 119 - 120: 29.698 distance: 119 - 125: 16.751 distance: 120 - 157: 19.292 distance: 121 - 122: 27.151 distance: 122 - 123: 25.375 distance: 123 - 124: 23.060 distance: 125 - 126: 17.171 distance: 126 - 127: 14.701 distance: 126 - 129: 10.681 distance: 127 - 128: 6.738 distance: 127 - 134: 11.357 distance: 128 - 171: 9.390 distance: 129 - 130: 37.853 distance: 130 - 131: 36.685 distance: 131 - 132: 6.028 distance: 132 - 133: 15.335 distance: 134 - 135: 11.274 distance: 135 - 136: 11.481 distance: 135 - 138: 15.573 distance: 136 - 137: 8.375 distance: 136 - 143: 9.534 distance: 137 - 179: 7.640 distance: 138 - 139: 10.879 distance: 139 - 140: 11.112 distance: 140 - 141: 3.492 distance: 141 - 142: 10.183 distance: 143 - 144: 5.216 distance: 144 - 145: 6.642 distance: 144 - 147: 7.417 distance: 145 - 146: 4.894 distance: 145 - 157: 4.084 distance: 146 - 187: 10.337 distance: 147 - 148: 5.527 distance: 148 - 149: 5.274 distance: 148 - 150: 10.132 distance: 149 - 151: 6.257 distance: 150 - 152: 15.772 distance: 150 - 153: 6.211 distance: 151 - 152: 11.855 distance: 152 - 154: 4.371 distance: 153 - 155: 5.640 distance: 154 - 156: 8.333 distance: 155 - 156: 5.272