Starting phenix.real_space_refine on Sat Nov 16 19:46:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hdz_34684/11_2024/8hdz_34684.cif" } resolution = 3.05 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= 0.020 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 62 5.16 5 C 7619 2.51 5 N 1951 2.21 5 O 2229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11861 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6622 Classifications: {'peptide': 813} Link IDs: {'PTRANS': 30, 'TRANS': 782} 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: 6.99, per 1000 atoms: 0.59 Number of scatterers: 11861 At special positions: 0 Unit cell: (92.4, 124.32, 141.96, 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 62 16.00 O 2229 8.00 N 1951 7.00 C 7619 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.6 seconds 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2782 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 17 sheets defined 36.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.670A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 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 removed outlier: 3.830A pdb=" N PHE A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 removed outlier: 3.939A pdb=" N THR A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.668A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.945A 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 497 through 514 removed outlier: 3.872A pdb=" N GLY A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.787A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 642 Processing helix chain 'A' and resid 646 through 665 Processing helix chain 'A' and resid 666 through 672 removed outlier: 3.880A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'C' and resid 8 through 11 Processing helix chain 'C' and resid 12 through 19 removed outlier: 3.881A pdb=" N LYS C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 4.484A pdb=" N LYS C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 147 through 159 removed outlier: 3.661A pdb=" N ILE C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 188 Processing helix chain 'C' and resid 249 through 257 removed outlier: 4.123A pdb=" N LYS C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 298 removed outlier: 3.570A pdb=" N VAL C 289 " --> pdb=" O THR C 285 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 323 removed outlier: 3.621A pdb=" N THR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 341 through 350 removed outlier: 3.565A pdb=" N LYS C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN C 350 " --> pdb=" O ARG C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.538A pdb=" N ASN C 374 " --> pdb=" O THR C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 396 removed outlier: 3.992A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.574A pdb=" N GLU C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 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 32 removed outlier: 4.212A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.664A pdb=" N PHE B 50 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.647A pdb=" N LYS B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE B 96 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 removed outlier: 3.828A pdb=" N LEU B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 194 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.604A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.070A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.654A pdb=" N SER A 73 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.133A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 165 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 302 Processing sheet with id=AA7, first strand: chain 'A' and resid 408 through 411 removed outlier: 3.825A pdb=" N LEU A 411 " --> pdb=" O GLY A 414 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 417 " --> pdb=" O PHE A 370 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 394 through 397 Processing sheet with id=AA9, first strand: chain 'A' and resid 732 through 734 removed outlier: 3.510A pdb=" N ARG A 713 " --> pdb=" O GLU A 706 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 706 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 755 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 548 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 547 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 61 through 65 removed outlier: 5.969A pdb=" N ARG C 207 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU C 63 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 69 through 70 removed outlier: 3.516A pdb=" N PHE C 69 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 166 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 87 removed outlier: 4.023A pdb=" N PHE C 126 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 128 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASP C 140 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 130 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N MET C 138 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 220 through 223 removed outlier: 5.352A pdb=" N ILE C 238 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 267 through 268 removed outlier: 3.597A pdb=" N LYS C 267 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 375 through 380 removed outlier: 5.996A pdb=" N GLU C 380 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 120 removed outlier: 5.731A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU B 155 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY B 179 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N CYS B 157 " --> pdb=" O GLY B 179 " (cutoff:3.500A) 443 hydrogen bonds defined for protein. 1269 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: 4.40 Time building geometry restraints manager: 3.18 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: 3780 1.34 - 1.46: 2569 1.46 - 1.58: 5678 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 12120 Sorted by residual: bond pdb=" C GLU A 93 " pdb=" O GLU A 93 " ideal model delta sigma weight residual 1.238 1.249 -0.011 1.28e-02 6.10e+03 7.83e-01 bond pdb=" C PRO A 593 " pdb=" N PRO A 594 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.19e-01 bond pdb=" CA ILE A 153 " pdb=" CB ILE A 153 " ideal model delta sigma weight residual 1.537 1.547 -0.010 1.29e-02 6.01e+03 6.11e-01 bond pdb=" CA LEU C 10 " pdb=" CB LEU C 10 " ideal model delta sigma weight residual 1.533 1.545 -0.012 1.66e-02 3.63e+03 5.28e-01 bond pdb=" CB PRO B 82 " pdb=" CG PRO B 82 " ideal model delta sigma weight residual 1.492 1.525 -0.033 5.00e-02 4.00e+02 4.31e-01 ... (remaining 12115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 16281 2.13 - 4.26: 94 4.26 - 6.39: 9 6.39 - 8.51: 2 8.51 - 10.64: 1 Bond angle restraints: 16387 Sorted by residual: angle pdb=" CA LEU C 10 " pdb=" CB LEU C 10 " pdb=" CG LEU C 10 " ideal model delta sigma weight residual 116.30 126.94 -10.64 3.50e+00 8.16e-02 9.25e+00 angle pdb=" CA LEU C 202 " pdb=" CB LEU C 202 " pdb=" CG LEU C 202 " ideal model delta sigma weight residual 116.30 124.50 -8.20 3.50e+00 8.16e-02 5.49e+00 angle pdb=" C GLU C 36 " pdb=" N TRP C 37 " pdb=" CA TRP C 37 " ideal model delta sigma weight residual 122.62 118.74 3.88 1.78e+00 3.16e-01 4.76e+00 angle pdb=" N ILE A 180 " pdb=" CA ILE A 180 " pdb=" C ILE A 180 " ideal model delta sigma weight residual 112.12 110.42 1.70 8.40e-01 1.42e+00 4.08e+00 angle pdb=" CA LEU A 517 " pdb=" CB LEU A 517 " pdb=" CG LEU A 517 " ideal model delta sigma weight residual 116.30 123.33 -7.03 3.50e+00 8.16e-02 4.03e+00 ... (remaining 16382 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.15: 6437 16.15 - 32.29: 704 32.29 - 48.44: 143 48.44 - 64.58: 27 64.58 - 80.73: 9 Dihedral angle restraints: 7320 sinusoidal: 3002 harmonic: 4318 Sorted by residual: dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N PRO B 71 " pdb=" CA PRO B 71 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA ASP C 178 " pdb=" CB ASP C 178 " pdb=" CG ASP C 178 " pdb=" OD1 ASP C 178 " ideal model delta sinusoidal sigma weight residual -30.00 -89.04 59.04 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 728 " pdb=" CB ASP A 728 " pdb=" CG ASP A 728 " pdb=" OD1 ASP A 728 " ideal model delta sinusoidal sigma weight residual -30.00 -89.00 59.00 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 7317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1098 0.027 - 0.054: 417 0.054 - 0.080: 160 0.080 - 0.107: 95 0.107 - 0.134: 47 Chirality restraints: 1817 Sorted by residual: chirality pdb=" CA ILE A 158 " pdb=" N ILE A 158 " pdb=" C ILE A 158 " pdb=" CB ILE A 158 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 516 " pdb=" N ILE A 516 " pdb=" C ILE A 516 " pdb=" CB ILE A 516 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-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 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 ... (remaining 1814 not shown) Planarity restraints: 2085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 592 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO A 593 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 593 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 593 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 45 " -0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO B 46 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 43 " 0.025 5.00e-02 4.00e+02 3.69e-02 2.17e+00 pdb=" N PRO B 44 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.021 5.00e-02 4.00e+02 ... (remaining 2082 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 407 2.72 - 3.26: 11714 3.26 - 3.81: 19147 3.81 - 4.35: 23103 4.35 - 4.90: 39529 Nonbonded interactions: 93900 Sorted by model distance: nonbonded pdb=" OH TYR C 302 " pdb=" O LEU C 361 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR A 190 " pdb=" OD2 ASP A 192 " model vdw 2.229 3.040 nonbonded pdb=" O LYS C 310 " pdb=" NE2 GLN C 318 " model vdw 2.232 3.120 nonbonded pdb=" ND2 ASN C 304 " pdb=" O GLY C 362 " model vdw 2.239 3.120 nonbonded pdb=" OG SER A 564 " pdb=" OE1 GLU A 566 " model vdw 2.239 3.040 ... (remaining 93895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.060 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: 0.000 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.980 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4673 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 0.033 12120 Z= 0.109 Angle : 0.437 10.643 16387 Z= 0.228 Chirality : 0.040 0.134 1817 Planarity : 0.003 0.049 2085 Dihedral : 13.939 80.731 4538 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1451 helix: 1.26 (0.25), residues: 474 sheet: 0.88 (0.34), residues: 258 loop : -0.96 (0.24), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 137 HIS 0.001 0.000 HIS A 36 PHE 0.007 0.001 PHE A 200 TYR 0.013 0.001 TYR B 70 ARG 0.003 0.000 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.406 Fit side-chains revert: symmetry clash REVERT: A 168 GLU cc_start: 0.5299 (mm-30) cc_final: 0.4629 (tm-30) REVERT: B 212 TRP cc_start: 0.3241 (m100) cc_final: 0.2938 (m100) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2634 time to fit residues: 55.3537 Evaluate side-chains 109 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12120 Z= 0.315 Angle : 0.669 12.772 16387 Z= 0.346 Chirality : 0.047 0.168 1817 Planarity : 0.005 0.070 2085 Dihedral : 4.432 20.009 1604 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 0.97 % Allowed : 11.04 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.22), residues: 1451 helix: 0.67 (0.24), residues: 470 sheet: 0.64 (0.34), residues: 245 loop : -1.20 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 37 HIS 0.013 0.002 HIS A 170 PHE 0.018 0.002 PHE C 414 TYR 0.035 0.002 TYR A 190 ARG 0.007 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.2861 (mtt) cc_final: 0.2651 (mtt) REVERT: A 787 PHE cc_start: 0.5551 (m-80) cc_final: 0.5179 (m-80) outliers start: 13 outliers final: 12 residues processed: 118 average time/residue: 0.2484 time to fit residues: 43.9085 Evaluate side-chains 110 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.0170 chunk 40 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 overall best weight: 4.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN C 393 ASN B 8 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5264 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.149 12120 Z= 0.603 Angle : 0.926 14.348 16387 Z= 0.489 Chirality : 0.056 0.278 1817 Planarity : 0.007 0.079 2085 Dihedral : 5.892 25.565 1604 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.69 % Rotamer: Outliers : 3.43 % Allowed : 15.75 % Favored : 80.82 % 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: -1.76 (0.21), residues: 1451 helix: -0.69 (0.23), residues: 457 sheet: -0.33 (0.34), residues: 246 loop : -1.77 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP C 37 HIS 0.012 0.003 HIS A 319 PHE 0.037 0.003 PHE C 414 TYR 0.040 0.004 TYR A 300 ARG 0.009 0.001 ARG A 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.5666 (tptt) cc_final: 0.5445 (pttm) REVERT: A 88 MET cc_start: 0.4112 (mtt) cc_final: 0.3908 (mtt) REVERT: A 334 PHE cc_start: 0.6592 (OUTLIER) cc_final: 0.6169 (t80) REVERT: A 455 MET cc_start: 0.3500 (mtt) cc_final: 0.3215 (mtt) REVERT: C 294 ILE cc_start: -0.1010 (OUTLIER) cc_final: -0.1584 (tt) REVERT: C 339 ASN cc_start: 0.4365 (t0) cc_final: 0.4162 (t0) REVERT: B 23 MET cc_start: 0.3580 (tpp) cc_final: 0.3235 (ptm) REVERT: B 29 PHE cc_start: 0.5332 (m-80) cc_final: 0.4458 (t80) outliers start: 46 outliers final: 31 residues processed: 155 average time/residue: 0.2343 time to fit residues: 53.8011 Evaluate side-chains 148 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 480 ASP Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 693 ARG Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 383 LYS Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 657 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 12120 Z= 0.274 Angle : 0.639 10.152 16387 Z= 0.335 Chirality : 0.045 0.193 1817 Planarity : 0.005 0.068 2085 Dihedral : 4.938 20.698 1604 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.39 % Allowed : 18.58 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1451 helix: -0.13 (0.24), residues: 461 sheet: -0.16 (0.35), residues: 236 loop : -1.61 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 37 HIS 0.007 0.001 HIS A 170 PHE 0.024 0.002 PHE C 308 TYR 0.025 0.002 TYR A 190 ARG 0.005 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.292 Fit side-chains revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.5815 (t80) REVERT: A 416 LYS cc_start: 0.7159 (OUTLIER) cc_final: 0.6500 (mmmt) REVERT: A 611 GLU cc_start: 0.5552 (tt0) cc_final: 0.5313 (tt0) REVERT: A 809 MET cc_start: 0.3258 (tpt) cc_final: 0.3040 (tpp) REVERT: C 339 ASN cc_start: 0.4191 (t0) cc_final: 0.3910 (t0) REVERT: B 23 MET cc_start: 0.3613 (tpp) cc_final: 0.3315 (ptm) REVERT: B 29 PHE cc_start: 0.5682 (m-80) cc_final: 0.4474 (t80) outliers start: 32 outliers final: 19 residues processed: 144 average time/residue: 0.2427 time to fit residues: 53.2488 Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 103 optimal weight: 0.0770 chunk 57 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN C 374 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5001 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12120 Z= 0.181 Angle : 0.560 10.615 16387 Z= 0.292 Chirality : 0.043 0.176 1817 Planarity : 0.004 0.066 2085 Dihedral : 4.460 19.647 1604 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.09 % Allowed : 19.48 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.22), residues: 1451 helix: 0.44 (0.25), residues: 464 sheet: -0.13 (0.35), residues: 233 loop : -1.37 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 37 HIS 0.009 0.001 HIS A 265 PHE 0.020 0.001 PHE C 308 TYR 0.020 0.001 TYR A 190 ARG 0.007 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.5764 (t80) REVERT: A 416 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6949 (mmtm) REVERT: C 339 ASN cc_start: 0.4137 (t0) cc_final: 0.3823 (t0) REVERT: B 23 MET cc_start: 0.3530 (tpp) cc_final: 0.3249 (ptm) REVERT: B 29 PHE cc_start: 0.5745 (m-80) cc_final: 0.4423 (t80) outliers start: 28 outliers final: 17 residues processed: 141 average time/residue: 0.2297 time to fit residues: 48.8002 Evaluate side-chains 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 115 optimal weight: 0.0980 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 0.0050 chunk 134 optimal weight: 1.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5020 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12120 Z= 0.200 Angle : 0.566 10.559 16387 Z= 0.294 Chirality : 0.044 0.181 1817 Planarity : 0.004 0.064 2085 Dihedral : 4.405 19.302 1604 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.99 % Allowed : 19.03 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1451 helix: 0.57 (0.25), residues: 463 sheet: -0.06 (0.35), residues: 233 loop : -1.29 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.005 0.001 HIS B 16 PHE 0.016 0.001 PHE C 410 TYR 0.023 0.001 TYR A 190 ARG 0.007 0.000 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6533 (OUTLIER) cc_final: 0.5842 (t80) REVERT: A 416 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6461 (mmmt) REVERT: A 497 ARG cc_start: 0.5231 (mmm160) cc_final: 0.3566 (ttt-90) REVERT: C 339 ASN cc_start: 0.4167 (t0) cc_final: 0.3845 (t0) REVERT: B 23 MET cc_start: 0.3480 (tpp) cc_final: 0.3195 (ptm) REVERT: B 29 PHE cc_start: 0.5773 (m-80) cc_final: 0.4411 (t80) outliers start: 40 outliers final: 31 residues processed: 145 average time/residue: 0.2164 time to fit residues: 48.2509 Evaluate side-chains 145 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 77 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4941 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12120 Z= 0.151 Angle : 0.528 12.110 16387 Z= 0.274 Chirality : 0.043 0.189 1817 Planarity : 0.004 0.062 2085 Dihedral : 4.165 18.615 1604 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 2.46 % Allowed : 19.78 % Favored : 77.76 % 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: -0.54 (0.23), residues: 1451 helix: 0.76 (0.25), residues: 467 sheet: 0.03 (0.35), residues: 241 loop : -1.23 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.003 0.001 HIS A 265 PHE 0.027 0.001 PHE A 267 TYR 0.017 0.001 TYR A 190 ARG 0.008 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.5669 (OUTLIER) cc_final: 0.5463 (ttp-110) REVERT: A 63 MET cc_start: 0.5965 (OUTLIER) cc_final: 0.5648 (ttt) REVERT: A 497 ARG cc_start: 0.5081 (mmm160) cc_final: 0.3548 (ttt-90) REVERT: B 23 MET cc_start: 0.3644 (tpp) cc_final: 0.3385 (ptm) REVERT: B 147 HIS cc_start: 0.4785 (OUTLIER) cc_final: 0.4217 (t70) outliers start: 33 outliers final: 23 residues processed: 144 average time/residue: 0.2268 time to fit residues: 48.6550 Evaluate side-chains 139 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 109 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12120 Z= 0.345 Angle : 0.680 12.085 16387 Z= 0.356 Chirality : 0.047 0.262 1817 Planarity : 0.005 0.065 2085 Dihedral : 4.874 20.481 1604 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.44 % Favored : 92.49 % Rotamer: Outliers : 3.21 % Allowed : 19.78 % Favored : 77.01 % 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: -0.98 (0.22), residues: 1451 helix: 0.11 (0.24), residues: 464 sheet: 0.06 (0.36), residues: 218 loop : -1.35 (0.23), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 37 HIS 0.006 0.001 HIS A 319 PHE 0.028 0.002 PHE C 410 TYR 0.028 0.002 TYR A 190 ARG 0.005 0.001 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.5753 (tptt) cc_final: 0.5514 (pttm) REVERT: A 334 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.5865 (t80) REVERT: A 357 MET cc_start: 0.3635 (OUTLIER) cc_final: 0.3428 (mtm) REVERT: C 339 ASN cc_start: 0.4209 (t0) cc_final: 0.3964 (t0) REVERT: B 23 MET cc_start: 0.3842 (tpp) cc_final: 0.3495 (ptm) REVERT: B 29 PHE cc_start: 0.5297 (m-80) cc_final: 0.4033 (t80) REVERT: B 147 HIS cc_start: 0.4740 (OUTLIER) cc_final: 0.4204 (t70) outliers start: 43 outliers final: 34 residues processed: 147 average time/residue: 0.2265 time to fit residues: 51.1870 Evaluate side-chains 140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 PHE Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12120 Z= 0.335 Angle : 0.690 12.954 16387 Z= 0.358 Chirality : 0.047 0.194 1817 Planarity : 0.005 0.066 2085 Dihedral : 4.968 21.457 1604 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.24 % Favored : 92.69 % Rotamer: Outliers : 3.51 % Allowed : 20.45 % Favored : 76.04 % 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: -1.18 (0.22), residues: 1451 helix: -0.10 (0.24), residues: 463 sheet: -0.14 (0.36), residues: 223 loop : -1.41 (0.23), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 37 HIS 0.007 0.001 HIS B 133 PHE 0.025 0.002 PHE C 410 TYR 0.030 0.002 TYR A 190 ARG 0.009 0.001 ARG A 497 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 105 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5669 (t80) REVERT: A 416 LYS cc_start: 0.7294 (OUTLIER) cc_final: 0.6509 (mmmt) REVERT: A 497 ARG cc_start: 0.5324 (mmm160) cc_final: 0.3574 (ttt-90) REVERT: C 339 ASN cc_start: 0.4360 (t0) cc_final: 0.4151 (t0) REVERT: B 19 TRP cc_start: 0.1707 (OUTLIER) cc_final: 0.1301 (m-10) REVERT: B 29 PHE cc_start: 0.5459 (m-80) cc_final: 0.4044 (t80) REVERT: B 147 HIS cc_start: 0.4726 (OUTLIER) cc_final: 0.4331 (t70) outliers start: 47 outliers final: 37 residues processed: 140 average time/residue: 0.2123 time to fit residues: 45.9996 Evaluate side-chains 144 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 103 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 190 TYR Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 550 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 575 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 19 TRP Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 114 optimal weight: 0.0270 chunk 11 optimal weight: 0.5980 chunk 88 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5015 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12120 Z= 0.182 Angle : 0.590 12.739 16387 Z= 0.303 Chirality : 0.044 0.199 1817 Planarity : 0.005 0.066 2085 Dihedral : 4.476 20.260 1604 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.55 % Favored : 93.38 % Rotamer: Outliers : 2.16 % Allowed : 22.01 % Favored : 75.82 % 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: -0.82 (0.23), residues: 1451 helix: 0.29 (0.24), residues: 475 sheet: -0.02 (0.36), residues: 230 loop : -1.25 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS A 265 PHE 0.029 0.001 PHE C 410 TYR 0.019 0.001 TYR A 37 ARG 0.008 0.000 ARG A 497 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2902 Ramachandran restraints generated. 1451 Oldfield, 0 Emsley, 1451 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 497 ARG cc_start: 0.5133 (mmm160) cc_final: 0.3620 (ttt-90) REVERT: C 95 MET cc_start: 0.4503 (tpp) cc_final: 0.3018 (tpp) REVERT: C 339 ASN cc_start: 0.4307 (t0) cc_final: 0.4092 (t0) REVERT: B 29 PHE cc_start: 0.5178 (m-80) cc_final: 0.4297 (t80) REVERT: B 147 HIS cc_start: 0.4718 (OUTLIER) cc_final: 0.4200 (t70) outliers start: 29 outliers final: 24 residues processed: 132 average time/residue: 0.2213 time to fit residues: 44.8384 Evaluate side-chains 134 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain B residue 70 TYR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain B residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 105 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5369 r_free = 0.5369 target = 0.290521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5074 r_free = 0.5074 target = 0.246363 restraints weight = 12124.889| |-----------------------------------------------------------------------------| r_work (start): 0.5078 rms_B_bonded: 4.05 r_work: 0.4583 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5670 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12120 Z= 0.210 Angle : 0.599 12.429 16387 Z= 0.308 Chirality : 0.044 0.219 1817 Planarity : 0.005 0.064 2085 Dihedral : 4.480 21.327 1604 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 2.24 % Allowed : 21.79 % Favored : 75.97 % 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: -0.81 (0.23), residues: 1451 helix: 0.30 (0.24), residues: 476 sheet: -0.12 (0.35), residues: 239 loop : -1.22 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 212 HIS 0.004 0.001 HIS A 265 PHE 0.037 0.002 PHE C 410 TYR 0.022 0.001 TYR A 190 ARG 0.009 0.000 ARG A 497 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.52 seconds wall clock time: 48 minutes 21.46 seconds (2901.46 seconds total)