Starting phenix.real_space_refine on Tue Jun 10 16:43:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_34684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_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/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_34684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_34684.map" model { file = "/net/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_34684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hdz_34684/06_2025/8hdz_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-5710/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: 7.36, per 1000 atoms: 0.62 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: 2.99 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: 1.55 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: 3.57 Time building geometry restraints manager: 3.35 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: 2.370 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: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 28.870 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- 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= 0.086 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 Details of bonding type rmsd hydrogen bonds : bond 0.14542 ( 443) hydrogen bonds : angle 6.32479 ( 1269) covalent geometry : bond 0.00174 (12120) covalent geometry : angle 0.43686 (16387) *********************** 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 : 1.315 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: 0.2358 time to fit residues: 50.2318 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 : 1.323 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5408 r_free = 0.5408 target = 0.294407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.224197 restraints weight = 12301.793| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 2.57 r_work: 0.4587 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 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= 0.216 Angle : 0.669 12.776 16387 Z= 0.346 Chirality : 0.047 0.168 1817 Planarity : 0.005 0.069 2085 Dihedral : 4.432 20.013 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 Details of bonding type rmsd hydrogen bonds : bond 0.04954 ( 443) hydrogen bonds : angle 5.68381 ( 1269) covalent geometry : bond 0.00500 (12120) covalent geometry : angle 0.66937 (16387) *********************** 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 : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 PHE cc_start: 0.5629 (m-80) cc_final: 0.5084 (m-80) REVERT: C 138 MET cc_start: 0.4635 (tpp) cc_final: 0.4313 (tpp) outliers start: 13 outliers final: 12 residues processed: 118 average time/residue: 0.2822 time to fit residues: 50.2364 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 : 1.550 ------------------------------------------------------------------------------- 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 90 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.295169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.224195 restraints weight = 12486.307| |-----------------------------------------------------------------------------| r_work (start): 0.4808 rms_B_bonded: 2.51 r_work: 0.4614 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5517 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12120 Z= 0.164 Angle : 0.569 10.400 16387 Z= 0.298 Chirality : 0.044 0.172 1817 Planarity : 0.004 0.052 2085 Dihedral : 4.277 20.761 1604 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 1.72 % Allowed : 12.91 % Favored : 85.37 % 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: -0.43 (0.22), residues: 1451 helix: 0.67 (0.24), residues: 470 sheet: 0.49 (0.35), residues: 235 loop : -1.18 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 37 HIS 0.008 0.001 HIS A 170 PHE 0.014 0.001 PHE A 31 TYR 0.023 0.002 TYR A 190 ARG 0.004 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 443) hydrogen bonds : angle 5.43064 ( 1269) covalent geometry : bond 0.00377 (12120) covalent geometry : angle 0.56942 (16387) *********************** 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 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.6324 (t80) REVERT: A 787 PHE cc_start: 0.5483 (m-80) cc_final: 0.4908 (m-80) REVERT: C 138 MET cc_start: 0.4622 (tpp) cc_final: 0.4304 (tpp) outliers start: 23 outliers final: 13 residues processed: 122 average time/residue: 0.2275 time to fit residues: 41.7335 Evaluate side-chains 116 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE 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 334 PHE Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 112 ILE 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 20 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5433 r_free = 0.5433 target = 0.298096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.260842 restraints weight = 12136.412| |-----------------------------------------------------------------------------| r_work (start): 0.5178 rms_B_bonded: 2.32 r_work: 0.4755 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5435 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12120 Z= 0.118 Angle : 0.529 9.596 16387 Z= 0.273 Chirality : 0.043 0.161 1817 Planarity : 0.004 0.066 2085 Dihedral : 4.058 19.268 1604 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.31 % Favored : 94.62 % Rotamer: Outliers : 1.42 % Allowed : 15.52 % Favored : 83.06 % 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: -0.28 (0.23), residues: 1451 helix: 0.89 (0.25), residues: 471 sheet: 0.43 (0.35), residues: 242 loop : -1.13 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.007 0.001 HIS A 170 PHE 0.012 0.001 PHE C 410 TYR 0.019 0.001 TYR A 190 ARG 0.006 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 443) hydrogen bonds : angle 5.10416 ( 1269) covalent geometry : bond 0.00265 (12120) covalent geometry : angle 0.52872 (16387) *********************** 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 133 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6527 (OUTLIER) cc_final: 0.6166 (t80) REVERT: A 671 MET cc_start: 0.5460 (mtm) cc_final: 0.5225 (mtm) REVERT: C 138 MET cc_start: 0.5093 (tpp) cc_final: 0.4802 (tpp) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.3068 time to fit residues: 60.3739 Evaluate side-chains 118 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 368 MET 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 701 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 149 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 31 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5426 r_free = 0.5426 target = 0.296467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5156 r_free = 0.5156 target = 0.256301 restraints weight = 12396.253| |-----------------------------------------------------------------------------| r_work (start): 0.5145 rms_B_bonded: 3.14 r_work: 0.4671 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12120 Z= 0.127 Angle : 0.532 10.179 16387 Z= 0.274 Chirality : 0.043 0.173 1817 Planarity : 0.004 0.053 2085 Dihedral : 4.064 18.881 1604 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 1.94 % Allowed : 15.67 % Favored : 82.39 % 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: -0.27 (0.23), residues: 1451 helix: 0.91 (0.25), residues: 469 sheet: 0.34 (0.34), residues: 248 loop : -1.09 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 37 HIS 0.006 0.001 HIS A 170 PHE 0.010 0.001 PHE A 560 TYR 0.019 0.001 TYR A 190 ARG 0.007 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 443) hydrogen bonds : angle 5.07574 ( 1269) covalent geometry : bond 0.00290 (12120) covalent geometry : angle 0.53155 (16387) *********************** 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 138 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5371 (ttp-170) REVERT: A 334 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 494 PHE cc_start: 0.6982 (m-10) cc_final: 0.6782 (m-80) REVERT: C 138 MET cc_start: 0.5094 (tpp) cc_final: 0.4706 (tpp) REVERT: B 29 PHE cc_start: 0.4884 (m-80) cc_final: 0.3661 (t80) REVERT: B 195 PHE cc_start: 0.1227 (m-80) cc_final: 0.1013 (m-80) REVERT: B 212 TRP cc_start: 0.3547 (m100) cc_final: 0.3314 (m100) outliers start: 26 outliers final: 18 residues processed: 131 average time/residue: 0.2619 time to fit residues: 52.0546 Evaluate side-chains 128 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG 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 228 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 334 PHE 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 701 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain B residue 1 MET 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 112 ILE Chi-restraints excluded: chain B residue 149 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 143 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 C 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5376 r_free = 0.5376 target = 0.289637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.217010 restraints weight = 12451.972| |-----------------------------------------------------------------------------| r_work (start): 0.4738 rms_B_bonded: 2.63 r_work: 0.4522 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 12120 Z= 0.235 Angle : 0.691 13.431 16387 Z= 0.358 Chirality : 0.047 0.223 1817 Planarity : 0.005 0.075 2085 Dihedral : 4.840 21.474 1604 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 2.76 % Allowed : 16.72 % Favored : 80.52 % 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: -0.91 (0.22), residues: 1451 helix: 0.22 (0.24), residues: 467 sheet: 0.05 (0.35), residues: 233 loop : -1.36 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 37 HIS 0.009 0.002 HIS A 319 PHE 0.023 0.002 PHE C 414 TYR 0.026 0.002 TYR A 300 ARG 0.010 0.001 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 443) hydrogen bonds : angle 5.75147 ( 1269) covalent geometry : bond 0.00551 (12120) covalent geometry : angle 0.69083 (16387) *********************** 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 150 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6707 (OUTLIER) cc_final: 0.6143 (t80) REVERT: A 787 PHE cc_start: 0.6065 (m-80) cc_final: 0.5778 (m-80) REVERT: B 23 MET cc_start: 0.3483 (ptt) cc_final: 0.3191 (ptm) REVERT: B 29 PHE cc_start: 0.5012 (m-80) cc_final: 0.3595 (t80) REVERT: B 212 TRP cc_start: 0.3531 (m100) cc_final: 0.3258 (m100) outliers start: 37 outliers final: 29 residues processed: 139 average time/residue: 0.3400 time to fit residues: 71.5551 Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 261 THR 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 368 MET Chi-restraints excluded: chain A residue 417 VAL 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 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 701 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 369 ILE 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 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 64 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5422 r_free = 0.5422 target = 0.295615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.227114 restraints weight = 12407.642| |-----------------------------------------------------------------------------| r_work (start): 0.4828 rms_B_bonded: 2.65 r_work: 0.4616 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5447 moved from start: 0.3193 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= 0.125 Angle : 0.555 10.199 16387 Z= 0.286 Chirality : 0.043 0.201 1817 Planarity : 0.004 0.059 2085 Dihedral : 4.279 19.880 1604 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.44 % Favored : 94.42 % Rotamer: Outliers : 2.01 % Allowed : 17.91 % Favored : 80.07 % 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: -0.53 (0.23), residues: 1451 helix: 0.59 (0.24), residues: 474 sheet: 0.15 (0.36), residues: 232 loop : -1.14 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 37 HIS 0.006 0.001 HIS A 170 PHE 0.026 0.001 PHE A 267 TYR 0.016 0.001 TYR A 190 ARG 0.008 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 443) hydrogen bonds : angle 5.22468 ( 1269) covalent geometry : bond 0.00283 (12120) covalent geometry : angle 0.55526 (16387) *********************** 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 144 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.5932 (t80) REVERT: A 416 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6563 (mmmt) REVERT: A 497 ARG cc_start: 0.5352 (mmm160) cc_final: 0.3677 (ttt-90) REVERT: B 23 MET cc_start: 0.3623 (ptt) cc_final: 0.3296 (ptm) REVERT: B 29 PHE cc_start: 0.5076 (m-80) cc_final: 0.3605 (t80) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 0.2389 time to fit residues: 48.2170 Evaluate side-chains 131 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 477 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 399 SER 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 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 112 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5345 r_free = 0.5345 target = 0.285776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.211338 restraints weight = 12377.420| |-----------------------------------------------------------------------------| r_work (start): 0.4686 rms_B_bonded: 2.56 r_work: 0.4502 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5772 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.115 12120 Z= 0.323 Angle : 0.822 11.678 16387 Z= 0.432 Chirality : 0.052 0.308 1817 Planarity : 0.006 0.064 2085 Dihedral : 5.456 22.476 1604 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.65 % Favored : 92.21 % Rotamer: Outliers : 3.21 % Allowed : 17.91 % Favored : 78.88 % 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: -1.47 (0.22), residues: 1451 helix: -0.41 (0.23), residues: 469 sheet: -0.23 (0.36), residues: 216 loop : -1.56 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 37 HIS 0.012 0.002 HIS A 319 PHE 0.033 0.003 PHE C 414 TYR 0.033 0.003 TYR A 300 ARG 0.007 0.001 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.06114 ( 443) hydrogen bonds : angle 6.32600 ( 1269) covalent geometry : bond 0.00765 (12120) covalent geometry : angle 0.82150 (16387) *********************** 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 160 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.6046 (t80) REVERT: A 416 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6834 (mmtm) REVERT: A 787 PHE cc_start: 0.6497 (m-80) cc_final: 0.6290 (m-80) REVERT: B 23 MET cc_start: 0.3540 (ptt) cc_final: 0.3262 (ptm) REVERT: B 29 PHE cc_start: 0.5111 (m-80) cc_final: 0.3937 (t80) outliers start: 43 outliers final: 30 residues processed: 150 average time/residue: 0.2168 time to fit residues: 49.8094 Evaluate side-chains 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 105 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 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 335 ILE Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 416 LYS Chi-restraints excluded: chain A residue 417 VAL 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 550 TYR Chi-restraints excluded: chain A residue 574 SER Chi-restraints excluded: chain A residue 657 GLN Chi-restraints excluded: chain A residue 701 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 C residue 399 SER Chi-restraints excluded: chain B residue 7 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 59 ASN B 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5409 r_free = 0.5409 target = 0.294061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4862 r_free = 0.4862 target = 0.222445 restraints weight = 12384.863| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 2.83 r_work: 0.4578 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5519 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12120 Z= 0.138 Angle : 0.593 12.098 16387 Z= 0.308 Chirality : 0.044 0.212 1817 Planarity : 0.005 0.065 2085 Dihedral : 4.629 20.701 1604 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.72 % Favored : 94.14 % Rotamer: Outliers : 2.01 % Allowed : 19.48 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1451 helix: 0.24 (0.24), residues: 473 sheet: 0.12 (0.36), residues: 215 loop : -1.32 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 137 HIS 0.006 0.001 HIS A 265 PHE 0.014 0.001 PHE A 267 TYR 0.017 0.001 TYR A 190 ARG 0.009 0.001 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 443) hydrogen bonds : angle 5.47907 ( 1269) covalent geometry : bond 0.00315 (12120) covalent geometry : angle 0.59260 (16387) *********************** 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 147 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 370 PHE cc_start: 0.5864 (m-80) cc_final: 0.5236 (m-80) REVERT: A 416 LYS cc_start: 0.7287 (mmtm) cc_final: 0.6574 (mmmt) REVERT: A 497 ARG cc_start: 0.5317 (mmm160) cc_final: 0.3640 (ttt-90) REVERT: A 787 PHE cc_start: 0.6068 (m-80) cc_final: 0.5802 (m-80) REVERT: C 95 MET cc_start: 0.4211 (tpp) cc_final: 0.3643 (tpp) REVERT: C 425 PHE cc_start: 0.4283 (m-80) cc_final: 0.4007 (m-80) REVERT: B 23 MET cc_start: 0.3449 (ptt) cc_final: 0.3179 (ptm) REVERT: B 29 PHE cc_start: 0.4929 (m-80) cc_final: 0.3782 (t80) outliers start: 27 outliers final: 21 residues processed: 138 average time/residue: 0.2071 time to fit residues: 44.1996 Evaluate side-chains 132 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 103 THR Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 214 GLN 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 335 ILE Chi-restraints excluded: chain A residue 368 MET 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 610 SER 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 C residue 399 SER Chi-restraints excluded: chain B residue 70 TYR 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 19 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 120 optimal weight: 0.3980 chunk 111 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5437 r_free = 0.5437 target = 0.299707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.257839 restraints weight = 11960.882| |-----------------------------------------------------------------------------| r_work (start): 0.5134 rms_B_bonded: 3.25 r_work: 0.4687 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5549 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12120 Z= 0.111 Angle : 0.578 13.625 16387 Z= 0.294 Chirality : 0.043 0.202 1817 Planarity : 0.004 0.063 2085 Dihedral : 4.271 18.208 1604 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.65 % Favored : 94.21 % Rotamer: Outliers : 1.42 % Allowed : 20.45 % Favored : 78.13 % 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: -0.53 (0.23), residues: 1451 helix: 0.64 (0.24), residues: 476 sheet: 0.13 (0.35), residues: 232 loop : -1.17 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 137 HIS 0.007 0.001 HIS A 265 PHE 0.033 0.001 PHE A 267 TYR 0.015 0.001 TYR A 190 ARG 0.008 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 443) hydrogen bonds : angle 5.15243 ( 1269) covalent geometry : bond 0.00247 (12120) covalent geometry : angle 0.57765 (16387) ********************** 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 137 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6512 (mm-30) REVERT: A 63 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5476 (ttt) REVERT: A 370 PHE cc_start: 0.5833 (m-80) cc_final: 0.5230 (m-80) REVERT: A 497 ARG cc_start: 0.4934 (mmm160) cc_final: 0.3555 (ttt-90) REVERT: C 95 MET cc_start: 0.4245 (tpp) cc_final: 0.3560 (tpp) REVERT: C 425 PHE cc_start: 0.4133 (m-80) cc_final: 0.3746 (m-10) REVERT: B 23 MET cc_start: 0.3478 (ptt) cc_final: 0.3070 (ptm) REVERT: B 29 PHE cc_start: 0.5055 (m-80) cc_final: 0.3916 (t80) outliers start: 19 outliers final: 16 residues processed: 131 average time/residue: 0.2083 time to fit residues: 42.0604 Evaluate side-chains 133 residues out of total 1340 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 165 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 368 MET 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 516 ILE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 294 ILE 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 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 134 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 0.0870 chunk 7 optimal weight: 0.0070 chunk 56 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 170 HIS ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5478 r_free = 0.5478 target = 0.303887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5193 r_free = 0.5193 target = 0.260793 restraints weight = 12145.351| |-----------------------------------------------------------------------------| r_work (start): 0.5181 rms_B_bonded: 3.64 r_work: 0.4713 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12120 Z= 0.102 Angle : 0.550 13.097 16387 Z= 0.278 Chirality : 0.042 0.195 1817 Planarity : 0.004 0.061 2085 Dihedral : 4.036 18.429 1604 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.48 % Favored : 95.38 % Rotamer: Outliers : 1.72 % Allowed : 20.07 % Favored : 78.21 % 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: -0.28 (0.23), residues: 1451 helix: 0.84 (0.24), residues: 483 sheet: 0.13 (0.35), residues: 240 loop : -0.98 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 37 HIS 0.004 0.001 HIS A 170 PHE 0.024 0.001 PHE A 267 TYR 0.020 0.001 TYR A 162 ARG 0.008 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.03178 ( 443) hydrogen bonds : angle 4.93026 ( 1269) covalent geometry : bond 0.00226 (12120) covalent geometry : angle 0.55020 (16387) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8674.42 seconds wall clock time: 153 minutes 28.42 seconds (9208.42 seconds total)