Starting phenix.real_space_refine on Sat Jan 20 02:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hoy_34927/01_2024/8hoy_34927.pdb" } resolution = 2.76 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= 0.024 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 72 5.16 5 C 8624 2.51 5 N 2229 2.21 5 O 2529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13454 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8215 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3467 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain: "B" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1772 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 13, 'TRANS': 204} Time building chain proxies: 7.42, per 1000 atoms: 0.55 Number of scatterers: 13454 At special positions: 0 Unit cell: (107.52, 125.16, 139.44, 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 72 16.00 O 2529 8.00 N 2229 7.00 C 8624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.5 seconds 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3158 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 16 sheets defined 38.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.507A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 281 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 373 through 377 removed outlier: 3.551A pdb=" N ASP A 377 " --> pdb=" O ASP A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.774A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.726A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 502 through 514 removed outlier: 3.702A pdb=" N LEU A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 512 " --> pdb=" O LYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.865A pdb=" N LYS A 642 " --> pdb=" O LYS A 638 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.654A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 702 Processing helix chain 'A' and resid 764 through 781 Processing helix chain 'A' and resid 836 through 854 removed outlier: 3.942A pdb=" N GLU A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 882 Processing helix chain 'A' and resid 908 through 915 removed outlier: 3.838A pdb=" N THR A 912 " --> pdb=" O MET A 908 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 942 Processing helix chain 'A' and resid 970 through 983 Processing helix chain 'A' and resid 986 through 997 removed outlier: 4.181A pdb=" N GLN A 994 " --> pdb=" O ILE A 990 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 997 " --> pdb=" O PHE A 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 5.958A pdb=" N GLU C 12 " --> pdb=" O THR C 8 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N LEU C 13 " --> pdb=" O ASN C 9 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 36 removed outlier: 3.713A pdb=" N ASN C 32 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N SER C 33 " --> pdb=" O GLU C 29 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 36 " --> pdb=" O ASN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.606A pdb=" N ASP C 59 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 177 through 188 removed outlier: 3.632A pdb=" N TYR C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.782A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.580A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.606A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 367 through 374 Processing helix chain 'C' and resid 392 through 396 removed outlier: 3.951A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.645A pdb=" N GLU C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.631A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 31 removed outlier: 4.316A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 39 removed outlier: 3.599A pdb=" N LEU B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.614A pdb=" N PHE B 49 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 165 through 170 removed outlier: 3.508A pdb=" N LYS B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 removed outlier: 3.507A pdb=" N ILE B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.670A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 5.149A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA4, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.412A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.258A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 303 removed outlier: 4.333A pdb=" N CYS A 298 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 360 removed outlier: 4.743A pdb=" N VAL A 417 " --> pdb=" O PHE A 370 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE A 410 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 732 through 734 removed outlier: 5.552A pdb=" N ASN A 703 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER A 747 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 166 through 168 removed outlier: 4.143A pdb=" N ILE C 197 " --> pdb=" O VAL C 210 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 210 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 199 " --> pdb=" O GLN C 208 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 124 through 132 removed outlier: 6.734A pdb=" N ILE C 124 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 143 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE C 126 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA C 141 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG C 128 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 222 through 223 removed outlier: 3.910A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR C 239 " --> pdb=" O LYS C 243 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 267 through 268 Processing sheet with id=AB5, first strand: chain 'C' and resid 375 through 380 removed outlier: 6.357A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.523A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 107 through 108 525 hydrogen bonds defined for protein. 1491 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: 4.70 Time building geometry restraints manager: 5.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4297 1.34 - 1.46: 2920 1.46 - 1.58: 6419 1.58 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 13746 Sorted by residual: bond pdb=" CB ASN C 9 " pdb=" CG ASN C 9 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.02e-01 bond pdb=" CA ASN C 9 " pdb=" CB ASN C 9 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.62e-02 3.81e+03 8.95e-01 bond pdb=" C CYS A 934 " pdb=" O CYS A 934 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 8.29e-01 bond pdb=" C ILE B 13 " pdb=" N THR B 14 " ideal model delta sigma weight residual 1.328 1.339 -0.011 1.30e-02 5.92e+03 7.72e-01 bond pdb=" C VAL A 938 " pdb=" N PRO A 939 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.64e-01 ... (remaining 13741 not shown) Histogram of bond angle deviations from ideal: 100.46 - 107.19: 342 107.19 - 113.92: 7624 113.92 - 120.65: 5548 120.65 - 127.39: 4971 127.39 - 134.12: 91 Bond angle restraints: 18576 Sorted by residual: angle pdb=" N ILE C 228 " pdb=" CA ILE C 228 " pdb=" C ILE C 228 " ideal model delta sigma weight residual 113.71 108.95 4.76 9.50e-01 1.11e+00 2.51e+01 angle pdb=" N GLU A 969 " pdb=" CA GLU A 969 " pdb=" C GLU A 969 " ideal model delta sigma weight residual 108.34 113.48 -5.14 1.31e+00 5.83e-01 1.54e+01 angle pdb=" N ILE A 729 " pdb=" CA ILE A 729 " pdb=" C ILE A 729 " ideal model delta sigma weight residual 113.20 109.72 3.48 9.60e-01 1.09e+00 1.32e+01 angle pdb=" N THR A 949 " pdb=" CA THR A 949 " pdb=" C THR A 949 " ideal model delta sigma weight residual 110.97 113.74 -2.77 1.09e+00 8.42e-01 6.44e+00 angle pdb=" N ILE C 162 " pdb=" CA ILE C 162 " pdb=" C ILE C 162 " ideal model delta sigma weight residual 108.05 110.91 -2.86 1.18e+00 7.18e-01 5.89e+00 ... (remaining 18571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 7477 17.11 - 34.22: 709 34.22 - 51.33: 117 51.33 - 68.43: 17 68.43 - 85.54: 4 Dihedral angle restraints: 8324 sinusoidal: 3427 harmonic: 4897 Sorted by residual: dihedral pdb=" CA ALA B 9 " pdb=" C ALA B 9 " pdb=" N PRO B 10 " pdb=" CA PRO B 10 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER B 43 " pdb=" C SER B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP A 654 " pdb=" CB ASP A 654 " pdb=" CG ASP A 654 " pdb=" OD1 ASP A 654 " ideal model delta sinusoidal sigma weight residual -30.00 -86.91 56.91 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 8321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1384 0.035 - 0.071: 480 0.071 - 0.106: 139 0.106 - 0.141: 48 0.141 - 0.177: 3 Chirality restraints: 2054 Sorted by residual: chirality pdb=" CB ILE C 313 " pdb=" CA ILE C 313 " pdb=" CG1 ILE C 313 " pdb=" CG2 ILE C 313 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CB THR A 949 " pdb=" CA THR A 949 " pdb=" OG1 THR A 949 " pdb=" CG2 THR A 949 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE C 77 " pdb=" N ILE C 77 " pdb=" C ILE C 77 " pdb=" CB ILE C 77 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2051 not shown) Planarity restraints: 2366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 168 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ILE C 168 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE C 168 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU C 169 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 593 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.19e+00 pdb=" N PRO A 594 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 594 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 594 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 9 " -0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO B 10 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " -0.028 5.00e-02 4.00e+02 ... (remaining 2363 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 651 2.73 - 3.27: 13527 3.27 - 3.82: 22212 3.82 - 4.36: 26919 4.36 - 4.90: 44830 Nonbonded interactions: 108139 Sorted by model distance: nonbonded pdb=" OH TYR C 363 " pdb=" OD1 ASN C 406 " model vdw 2.189 2.440 nonbonded pdb=" O LEU A 988 " pdb=" OG SER A 991 " model vdw 2.200 2.440 nonbonded pdb=" OG1 THR A 391 " pdb=" OH TYR A 468 " model vdw 2.204 2.440 nonbonded pdb=" O PRO A 527 " pdb=" OH TYR A 681 " model vdw 2.219 2.440 nonbonded pdb=" OG SER A 564 " pdb=" OE1 GLU A 566 " model vdw 2.223 2.440 ... (remaining 108134 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.410 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: 7.710 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 39.020 Find NCS groups from input model: 0.360 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:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5276 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 : 0.002 0.029 13746 Z= 0.122 Angle : 0.463 6.586 18576 Z= 0.257 Chirality : 0.041 0.177 2054 Planarity : 0.004 0.051 2366 Dihedral : 13.252 85.543 5166 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.36 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.64 (0.21), residues: 1644 helix: 1.35 (0.23), residues: 565 sheet: -0.20 (0.35), residues: 234 loop : -1.82 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.002 0.000 HIS A 170 PHE 0.012 0.001 PHE A 433 TYR 0.013 0.001 TYR A 190 ARG 0.003 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ARG cc_start: 0.5799 (ttt180) cc_final: 0.5561 (tpt-90) REVERT: A 211 GLN cc_start: 0.4798 (pm20) cc_final: 0.4585 (mp10) REVERT: A 357 MET cc_start: 0.5718 (mmm) cc_final: 0.5242 (mmt) REVERT: A 516 ILE cc_start: 0.5145 (mt) cc_final: 0.4920 (mt) REVERT: C 98 LEU cc_start: 0.5734 (mt) cc_final: 0.5377 (tt) REVERT: B 164 SER cc_start: 0.7617 (p) cc_final: 0.7337 (m) outliers start: 0 outliers final: 2 residues processed: 274 average time/residue: 1.1536 time to fit residues: 349.0485 Evaluate side-chains 160 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 233 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 66 optimal weight: 0.5980 chunk 127 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN A 101 ASN A 296 HIS A 461 HIS A 544 ASN A 551 ASN A 556 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 825 ASN A 915 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 339 ASN ** C 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5642 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13746 Z= 0.332 Angle : 0.693 9.495 18576 Z= 0.368 Chirality : 0.048 0.204 2054 Planarity : 0.006 0.105 2366 Dihedral : 4.789 27.303 1826 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.94 % Favored : 91.00 % Rotamer: Outliers : 3.48 % Allowed : 12.41 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1644 helix: 0.36 (0.22), residues: 582 sheet: -0.63 (0.35), residues: 206 loop : -2.08 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 470 HIS 0.011 0.002 HIS A 170 PHE 0.025 0.002 PHE A 107 TYR 0.031 0.002 TYR A 190 ARG 0.008 0.001 ARG C 255 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 156 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASN cc_start: 0.7970 (p0) cc_final: 0.7741 (p0) REVERT: A 357 MET cc_start: 0.5744 (mmm) cc_final: 0.5178 (mmt) REVERT: A 457 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5948 (mtp180) REVERT: A 722 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4321 (p90) REVERT: B 164 SER cc_start: 0.7804 (p) cc_final: 0.7541 (m) outliers start: 53 outliers final: 23 residues processed: 187 average time/residue: 0.9929 time to fit residues: 209.0310 Evaluate side-chains 147 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 722 PHE Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 395 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 160 optimal weight: 0.0770 chunk 132 optimal weight: 10.0000 chunk 147 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 551 ASN ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 607 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 409 GLN ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13746 Z= 0.223 Angle : 0.599 9.335 18576 Z= 0.315 Chirality : 0.044 0.185 2054 Planarity : 0.005 0.075 2366 Dihedral : 4.558 23.021 1822 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.09 % Favored : 91.79 % Rotamer: Outliers : 3.68 % Allowed : 15.36 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.20), residues: 1644 helix: 0.34 (0.22), residues: 579 sheet: -0.87 (0.34), residues: 207 loop : -2.15 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 212 HIS 0.005 0.001 HIS A 170 PHE 0.024 0.002 PHE C 188 TYR 0.021 0.001 TYR A 658 ARG 0.005 0.000 ARG C 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3288 Ramachandran restraints generated. 1644 Oldfield, 0 Emsley, 1644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 141 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.5683 (mmm) cc_final: 0.5092 (mmt) REVERT: C 184 MET cc_start: 0.5464 (mmm) cc_final: 0.4917 (mmm) REVERT: B 164 SER cc_start: 0.7711 (p) cc_final: 0.7466 (m) REVERT: B 212 TRP cc_start: 0.6495 (m100) cc_final: 0.6239 (m100) outliers start: 56 outliers final: 24 residues processed: 179 average time/residue: 0.9108 time to fit residues: 184.7858 Evaluate side-chains 146 residues out of total 1524 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 219 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 181 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 0.9990 chunk 111 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 296 HIS ** A 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 825 ASN ** C 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.3040 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: