Starting phenix.real_space_refine on Thu Jul 2 12:52:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903.map" model { file = "/net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vap_64903/07_2026/9vap_64903_neut.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.038 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: 7 Type Number sf(0) Gaussians W 1 12.54 5 Fe 20 7.16 5 P 4 5.49 5 S 87 5.16 5 C 5286 2.51 5 N 1476 2.21 5 O 1585 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8459 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 896, 7066 Classifications: {'peptide': 896} Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 846} Chain: "B" Number of atoms: 1257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1257 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 7, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 103 Ad-hoc single atom residues: {' W': 1} Unusual residues: {'H2S': 1, 'MGD': 2, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 32 Unusual residues: {'SF4': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 139 SG CYS A 71 47.219 45.922 53.657 1.00143.08 S ATOM 162 SG CYS A 75 53.359 45.486 54.770 1.00130.15 S ATOM 117 SG CYS A 68 49.917 41.591 57.713 1.00127.14 S ATOM 377 SG CYS A 103 48.768 47.467 59.559 1.00132.52 S ATOM 1095 SG CYS A 193 36.886 45.441 47.577 1.00135.72 S ATOM 8152 SG CYS B 157 57.417 54.757 62.041 1.00146.60 S ATOM 7190 SG CYS B 19 53.558 54.178 67.156 1.00146.49 S ATOM 7172 SG CYS B 16 51.398 53.901 61.425 1.00152.19 S ATOM 7149 SG CYS B 13 53.153 59.557 63.985 1.00145.29 S ATOM 7498 SG CYS B 60 63.748 62.955 80.408 1.00218.95 S ATOM 7531 SG CYS B 65 62.691 59.611 85.689 1.00213.44 S ATOM 7474 SG CYS B 57 61.747 57.063 79.826 1.00170.08 S ATOM 7789 SG CYS B 99 57.614 61.511 82.141 1.00205.62 S ATOM 7883 SG CYS B 121 59.960 52.881 76.329 1.00161.54 S ATOM 7907 SG CYS B 124 62.495 47.158 73.354 1.00150.29 S ATOM 8124 SG CYS B 153 60.275 52.097 70.369 1.00155.15 S ATOM 7215 SG CYS B 23 56.344 48.397 74.407 1.00162.27 S ATOM 7733 SG CYS B 92 56.586 56.587 95.812 1.00239.99 S ATOM 7755 SG CYS B 95 57.807 57.344 90.209 1.00229.33 S ATOM 7715 SG CYS B 89 58.241 51.228 92.184 1.00221.69 S ATOM 7557 SG CYS B 69 62.543 55.910 93.890 1.00228.91 S Time building chain proxies: 1.44, per 1000 atoms: 0.17 Number of scatterers: 8459 At special positions: 0 Unit cell: (85.85, 88.4, 106.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 87 16.00 P 4 15.00 O 1585 8.00 N 1476 7.00 C 5286 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: 0.75 Conformation dependent library (CDL) restraints added in 373.4 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1103 " pdb="FE1 SF4 A1103 " - pdb=" SG CYS A 71 " pdb="FE3 SF4 A1103 " - pdb=" SG CYS A 68 " pdb="FE4 SF4 A1103 " - pdb=" SG CYS A 103 " pdb="FE2 SF4 A1103 " - pdb=" SG CYS A 75 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 13 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 157 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 19 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 16 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 99 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 65 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 57 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 60 " pdb=" SF4 B 303 " pdb="FE1 SF4 B 303 " - pdb=" SG CYS B 121 " pdb="FE2 SF4 B 303 " - pdb=" SG CYS B 124 " pdb="FE4 SF4 B 303 " - pdb=" SG CYS B 23 " pdb="FE3 SF4 B 303 " - pdb=" SG CYS B 153 " pdb=" SF4 B 304 " pdb="FE2 SF4 B 304 " - pdb=" SG CYS B 95 " pdb="FE4 SF4 B 304 " - pdb=" SG CYS B 69 " pdb="FE3 SF4 B 304 " - pdb=" SG CYS B 89 " pdb="FE1 SF4 B 304 " - pdb=" SG CYS B 92 " Number of angles added : 60 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1924 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 10 sheets defined 39.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.926A pdb=" N LEU A 109 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ARG A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Processing helix chain 'A' and resid 154 through 156 No H-bonds generated for 'chain 'A' and resid 154 through 156' Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 214 through 220 Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 246 removed outlier: 4.165A pdb=" N HIS A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 275 through 291 removed outlier: 3.693A pdb=" N PHE A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.693A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 327 through 341 removed outlier: 3.586A pdb=" N THR A 341 " --> pdb=" O MET A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.668A pdb=" N THR A 353 " --> pdb=" O CYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 373 Processing helix chain 'A' and resid 390 through 397 Processing helix chain 'A' and resid 411 through 423 Processing helix chain 'A' and resid 425 through 432 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 453 through 460 Processing helix chain 'A' and resid 486 through 497 Processing helix chain 'A' and resid 508 through 512 Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.559A pdb=" N THR A 531 " --> pdb=" O GLN A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 570 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 587 through 596 Processing helix chain 'A' and resid 608 through 618 Processing helix chain 'A' and resid 619 through 622 removed outlier: 3.963A pdb=" N PHE A 622 " --> pdb=" O TRP A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 779 through 783 removed outlier: 3.500A pdb=" N VAL A 783 " --> pdb=" O ARG A 780 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 removed outlier: 3.681A pdb=" N GLN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 812 removed outlier: 4.106A pdb=" N LYS A 811 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 834 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.619A pdb=" N GLU A 840 " --> pdb=" O PRO A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 858 Processing helix chain 'A' and resid 905 through 909 removed outlier: 3.533A pdb=" N TYR A 909 " --> pdb=" O ALA A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 925 removed outlier: 3.515A pdb=" N THR A 924 " --> pdb=" O SER A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 4.097A pdb=" N CYS B 23 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 removed outlier: 3.613A pdb=" N LEU B 31 " --> pdb=" O ASP B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 64 through 69 removed outlier: 3.916A pdb=" N CYS B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 151 through 156 removed outlier: 3.695A pdb=" N GLU B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 156' Processing helix chain 'B' and resid 166 through 180 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 67 removed outlier: 6.654A pdb=" N GLN A 82 " --> pdb=" O TRP A 86 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TRP A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132 removed outlier: 4.563A pdb=" N VAL A 520 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL A 500 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU A 523 " --> pdb=" O VAL A 500 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 502 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 474 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 503 " --> pdb=" O PHE A 476 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TYR A 159 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TRP A 477 " --> pdb=" O TYR A 159 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N MET A 161 " --> pdb=" O TRP A 477 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N ASP A 187 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE A 160 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 269 removed outlier: 6.773A pdb=" N ILE A 251 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL A 269 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 253 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS A 222 " --> pdb=" O SER A 345 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 347 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 224 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 381 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP A 348 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 533 through 536 Processing sheet with id=AA5, first strand: chain 'A' and resid 581 through 582 Processing sheet with id=AA6, first strand: chain 'A' and resid 792 through 793 Processing sheet with id=AA7, first strand: chain 'A' and resid 815 through 820 removed outlier: 6.767A pdb=" N PHE A 846 " --> pdb=" O PRO A 893 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 8 Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 42 Processing sheet with id=AB1, first strand: chain 'B' and resid 74 through 76 283 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 3722 1.43 - 1.64: 4817 1.64 - 1.86: 102 1.86 - 2.07: 0 2.07 - 2.28: 60 Bond restraints: 8701 Sorted by residual: bond pdb=" N ILE A 192 " pdb=" CA ILE A 192 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.95e+00 bond pdb=" CB GLU A 116 " pdb=" CG GLU A 116 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB GLU B 134 " pdb=" CG GLU B 134 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.57e+00 bond pdb=" CB GLN B 176 " pdb=" CG GLN B 176 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CA ILE A 192 " pdb=" C ILE A 192 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.31e-02 5.83e+03 9.04e-01 ... (remaining 8696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 11692 2.20 - 4.40: 135 4.40 - 6.60: 14 6.60 - 8.81: 0 8.81 - 11.01: 2 Bond angle restraints: 11843 Sorted by residual: angle pdb=" CA GLN B 176 " pdb=" CB GLN B 176 " pdb=" CG GLN B 176 " ideal model delta sigma weight residual 114.10 120.69 -6.59 2.00e+00 2.50e-01 1.09e+01 angle pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " pdb=" CG GLU A 116 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.00e+01 angle pdb=" CB GLU A 116 " pdb=" CG GLU A 116 " pdb=" CD GLU A 116 " ideal model delta sigma weight residual 112.60 117.88 -5.28 1.70e+00 3.46e-01 9.64e+00 angle pdb=" CB MET A 350 " pdb=" CG MET A 350 " pdb=" SD MET A 350 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" CB GLN B 176 " pdb=" CG GLN B 176 " pdb=" CD GLN B 176 " ideal model delta sigma weight residual 112.60 117.57 -4.97 1.70e+00 3.46e-01 8.56e+00 ... (remaining 11838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 4575 20.64 - 41.28: 467 41.28 - 61.93: 110 61.93 - 82.57: 19 82.57 - 103.21: 4 Dihedral angle restraints: 5175 sinusoidal: 2152 harmonic: 3023 Sorted by residual: dihedral pdb=" CA GLU B 130 " pdb=" C GLU B 130 " pdb=" N THR B 131 " pdb=" CA THR B 131 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLU A 484 " pdb=" C GLU A 484 " pdb=" N THR A 485 " pdb=" CA THR A 485 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU A 552 " pdb=" C LEU A 552 " pdb=" N PHE A 553 " pdb=" CA PHE A 553 " ideal model delta harmonic sigma weight residual -180.00 -160.41 -19.59 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 5172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 726 0.030 - 0.061: 318 0.061 - 0.091: 109 0.091 - 0.121: 71 0.121 - 0.151: 14 Chirality restraints: 1238 Sorted by residual: chirality pdb=" CA ILE A 192 " pdb=" N ILE A 192 " pdb=" C ILE A 192 " pdb=" CB ILE A 192 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA PRO A 751 " pdb=" N PRO A 751 " pdb=" C PRO A 751 " pdb=" CB PRO A 751 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 1235 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 134 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" CD GLU B 134 " 0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU B 134 " -0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU B 134 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 150 " 0.029 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO B 151 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 151 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 151 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 116 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" CD GLU A 116 " -0.031 2.00e-02 2.50e+03 pdb=" OE1 GLU A 116 " 0.011 2.00e-02 2.50e+03 pdb=" OE2 GLU A 116 " 0.011 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1761 2.78 - 3.31: 7327 3.31 - 3.84: 13260 3.84 - 4.37: 16617 4.37 - 4.90: 28988 Nonbonded interactions: 67953 Sorted by model distance: nonbonded pdb=" S13 MGD A1102 " pdb=" W W A1105 " model vdw 2.245 3.280 nonbonded pdb=" S13 MGD A1101 " pdb=" W W A1105 " model vdw 2.333 3.280 nonbonded pdb=" N GLU A 116 " pdb=" OE1 GLU A 116 " model vdw 2.476 3.120 nonbonded pdb=" S H2S A1104 " pdb=" W W A1105 " model vdw 2.495 3.280 nonbonded pdb=" SG CYS A 193 " pdb=" W W A1105 " model vdw 2.540 3.280 ... (remaining 67948 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.740 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:6.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 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 : 0.003 0.042 8721 Z= 0.132 Angle : 0.852 23.781 11903 Z= 0.295 Chirality : 0.044 0.151 1238 Planarity : 0.004 0.045 1521 Dihedral : 17.243 103.212 3251 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 1.48 % Allowed : 22.59 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.26), residues: 1057 helix: 1.24 (0.31), residues: 303 sheet: 0.26 (0.43), residues: 153 loop : -0.87 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 860 TYR 0.018 0.001 TYR A 595 PHE 0.006 0.001 PHE A 475 TRP 0.009 0.001 TRP A 348 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8701) covalent geometry : angle 0.55580 / 0.29 (11843) hydrogen bonds : bond 0.19494 / 13.32 ( 283) hydrogen bonds : angle 6.24360 / 4.48 ( 732) metal coordination : bond 0.00700 / 0.40 ( 20) metal coordination : angle 9.11115 / 6.64 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.322 Fit side-chains REVERT: A 58 ASN cc_start: 0.9328 (p0) cc_final: 0.8927 (p0) REVERT: B 24 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8364 (mptp) REVERT: B 32 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8379 (mm-30) REVERT: B 50 GLU cc_start: 0.8661 (tt0) cc_final: 0.8116 (tt0) REVERT: B 117 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.6627 (mtmt) REVERT: B 120 LYS cc_start: 0.9146 (pttp) cc_final: 0.8820 (tttp) REVERT: B 121 CYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8143 (t) REVERT: B 166 ASP cc_start: 0.8136 (p0) cc_final: 0.7917 (p0) outliers start: 13 outliers final: 6 residues processed: 100 average time/residue: 0.5542 time to fit residues: 58.8369 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 451 CYS Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain B residue 24 LYS Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain B residue 121 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.072675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.057472 restraints weight = 15288.266| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 2.57 r_work: 0.2533 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.044 8721 Z= 0.359 Angle : 0.994 25.937 11903 Z= 0.359 Chirality : 0.052 0.188 1238 Planarity : 0.005 0.047 1521 Dihedral : 10.134 98.468 1289 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 3.52 % Allowed : 20.43 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.26), residues: 1057 helix: 1.12 (0.31), residues: 315 sheet: 0.21 (0.43), residues: 151 loop : -0.94 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.024 0.002 TYR A 752 PHE 0.014 0.002 PHE A 475 TRP 0.013 0.001 TRP A 643 HIS 0.008 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.36 ( 8701) covalent geometry : angle 0.68973 / 0.35 (11843) hydrogen bonds : bond 0.06280 / 4.27 ( 283) hydrogen bonds : angle 5.39045 / 3.88 ( 732) metal coordination : bond 0.01887 / 1.21 ( 20) metal coordination : angle 10.11107 / 7.30 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.209 Fit side-chains REVERT: A 845 MET cc_start: 0.8901 (tpt) cc_final: 0.8480 (tpt) REVERT: A 848 GLU cc_start: 0.9299 (mt-10) cc_final: 0.9040 (mt-10) REVERT: B 32 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8397 (mm-30) REVERT: B 168 GLU cc_start: 0.8297 (pp20) cc_final: 0.7991 (tm-30) outliers start: 31 outliers final: 16 residues processed: 102 average time/residue: 0.5759 time to fit residues: 62.3581 Evaluate side-chains 99 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 33 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.061261 restraints weight = 14083.516| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.45 r_work: 0.2632 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8721 Z= 0.122 Angle : 0.862 23.740 11903 Z= 0.280 Chirality : 0.044 0.161 1238 Planarity : 0.004 0.047 1521 Dihedral : 9.557 100.343 1277 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 2.50 % Allowed : 22.70 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1057 helix: 1.32 (0.31), residues: 316 sheet: 0.24 (0.44), residues: 144 loop : -0.85 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 860 TYR 0.016 0.001 TYR A 595 PHE 0.010 0.001 PHE A 475 TRP 0.009 0.001 TRP A 418 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8701) covalent geometry : angle 0.53481 / 0.27 (11843) hydrogen bonds : bond 0.04265 / 2.93 ( 283) hydrogen bonds : angle 4.95564 / 3.58 ( 732) metal coordination : bond 0.00622 / 0.35 ( 20) metal coordination : angle 9.54149 / 6.92 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.303 Fit side-chains REVERT: A 845 MET cc_start: 0.8965 (tpt) cc_final: 0.8586 (tpt) REVERT: B 32 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8273 (mm-30) REVERT: B 50 GLU cc_start: 0.8776 (tt0) cc_final: 0.8212 (tt0) REVERT: B 105 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7311 (pm20) REVERT: B 121 CYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8269 (t) REVERT: B 166 ASP cc_start: 0.8026 (p0) cc_final: 0.7825 (p0) outliers start: 22 outliers final: 11 residues processed: 98 average time/residue: 0.6084 time to fit residues: 63.2811 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.060015 restraints weight = 14121.372| |-----------------------------------------------------------------------------| r_work (start): 0.2713 rms_B_bonded: 2.47 r_work: 0.2607 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2489 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8721 Z= 0.197 Angle : 0.889 24.580 11903 Z= 0.299 Chirality : 0.046 0.160 1238 Planarity : 0.004 0.045 1521 Dihedral : 9.611 98.352 1275 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 2.84 % Allowed : 22.70 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1057 helix: 1.39 (0.31), residues: 314 sheet: 0.22 (0.44), residues: 144 loop : -0.83 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.019 0.001 TYR A 595 PHE 0.011 0.001 PHE A 475 TRP 0.010 0.001 TRP A 643 HIS 0.006 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 ( 8701) covalent geometry : angle 0.57311 / 0.29 (11843) hydrogen bonds : bond 0.04684 / 3.21 ( 283) hydrogen bonds : angle 4.94323 / 3.57 ( 732) metal coordination : bond 0.01075 / 0.68 ( 20) metal coordination : angle 9.58844 / 6.96 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.340 Fit side-chains REVERT: A 845 MET cc_start: 0.8924 (tpt) cc_final: 0.8459 (tpt) REVERT: B 32 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8328 (mm-30) REVERT: B 50 GLU cc_start: 0.8758 (tt0) cc_final: 0.8273 (tt0) REVERT: B 121 CYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8368 (t) REVERT: B 168 GLU cc_start: 0.8362 (pp20) cc_final: 0.8022 (tm-30) outliers start: 25 outliers final: 16 residues processed: 100 average time/residue: 0.6396 time to fit residues: 67.8694 Evaluate side-chains 101 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 4 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 6.9990 chunk 50 optimal weight: 0.0870 chunk 59 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.074955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.059911 restraints weight = 14013.270| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.45 r_work: 0.2586 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 8721 Z= 0.201 Angle : 0.892 25.284 11903 Z= 0.300 Chirality : 0.046 0.162 1238 Planarity : 0.004 0.044 1521 Dihedral : 9.610 96.531 1274 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 3.41 % Allowed : 22.36 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1057 helix: 1.39 (0.31), residues: 314 sheet: 0.17 (0.44), residues: 144 loop : -0.84 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 860 TYR 0.019 0.001 TYR A 595 PHE 0.011 0.001 PHE A 475 TRP 0.010 0.001 TRP A 643 HIS 0.006 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 8701) covalent geometry : angle 0.57634 / 0.29 (11843) hydrogen bonds : bond 0.04680 / 3.20 ( 283) hydrogen bonds : angle 4.94129 / 3.57 ( 732) metal coordination : bond 0.01054 / 0.66 ( 20) metal coordination : angle 9.60913 / 6.98 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.331 Fit side-chains REVERT: A 845 MET cc_start: 0.8959 (tpt) cc_final: 0.8571 (tpt) REVERT: A 848 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8936 (mt-10) REVERT: B 32 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8336 (mm-30) REVERT: B 50 GLU cc_start: 0.8750 (tt0) cc_final: 0.8178 (tt0) REVERT: B 121 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8376 (t) REVERT: B 143 ASN cc_start: 0.9070 (t0) cc_final: 0.8777 (t0) REVERT: B 168 GLU cc_start: 0.8347 (pp20) cc_final: 0.7992 (tm-30) outliers start: 30 outliers final: 18 residues processed: 104 average time/residue: 0.6046 time to fit residues: 66.7812 Evaluate side-chains 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 45 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.0270 chunk 103 optimal weight: 0.3980 chunk 81 optimal weight: 0.0970 chunk 25 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN B 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.063769 restraints weight = 14429.925| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.45 r_work: 0.2721 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8721 Z= 0.087 Angle : 0.809 22.939 11903 Z= 0.259 Chirality : 0.042 0.136 1238 Planarity : 0.004 0.045 1521 Dihedral : 9.235 96.701 1274 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 1.93 % Allowed : 23.84 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.27), residues: 1057 helix: 1.41 (0.30), residues: 316 sheet: 0.22 (0.46), residues: 134 loop : -0.73 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 860 TYR 0.016 0.001 TYR A 595 PHE 0.017 0.001 PHE B 106 TRP 0.009 0.001 TRP A 348 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 8701) covalent geometry : angle 0.49736 / 0.25 (11843) hydrogen bonds : bond 0.03066 / 2.12 ( 283) hydrogen bonds : angle 4.60201 / 3.34 ( 732) metal coordination : bond 0.00475 / 0.26 ( 20) metal coordination : angle 8.99194 / 6.57 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.348 Fit side-chains REVERT: A 845 MET cc_start: 0.9012 (tpt) cc_final: 0.8588 (tpt) REVERT: A 848 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8849 (mt-10) REVERT: B 32 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8262 (mm-30) REVERT: B 50 GLU cc_start: 0.8848 (tt0) cc_final: 0.8301 (tt0) REVERT: B 120 LYS cc_start: 0.9306 (pttp) cc_final: 0.9077 (tttm) REVERT: B 143 ASN cc_start: 0.9118 (t0) cc_final: 0.8820 (t0) outliers start: 17 outliers final: 7 residues processed: 102 average time/residue: 0.6088 time to fit residues: 65.8422 Evaluate side-chains 89 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.075185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.059995 restraints weight = 14104.159| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 2.49 r_work: 0.2609 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8721 Z= 0.214 Angle : 0.892 25.164 11903 Z= 0.311 Chirality : 0.047 0.156 1238 Planarity : 0.004 0.042 1521 Dihedral : 9.495 93.522 1274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 2.50 % Allowed : 23.04 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1057 helix: 1.38 (0.30), residues: 318 sheet: 0.22 (0.45), residues: 143 loop : -0.91 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 38 TYR 0.020 0.001 TYR A 595 PHE 0.012 0.001 PHE A 475 TRP 0.010 0.001 TRP A 643 HIS 0.006 0.001 HIS A 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 ( 8701) covalent geometry : angle 0.60270 / 0.31 (11843) hydrogen bonds : bond 0.04626 / 3.17 ( 283) hydrogen bonds : angle 4.80333 / 3.48 ( 732) metal coordination : bond 0.01154 / 0.73 ( 20) metal coordination : angle 9.27279 / 6.74 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.322 Fit side-chains REVERT: A 848 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8887 (mt-10) REVERT: B 32 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8145 (mp0) REVERT: B 50 GLU cc_start: 0.8733 (tt0) cc_final: 0.8203 (tt0) REVERT: B 121 CYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8311 (t) REVERT: B 143 ASN cc_start: 0.9034 (t0) cc_final: 0.8725 (t0) REVERT: B 166 ASP cc_start: 0.7590 (p0) cc_final: 0.7333 (p0) outliers start: 22 outliers final: 13 residues processed: 102 average time/residue: 0.5973 time to fit residues: 64.6829 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 52 SER Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.076364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.061439 restraints weight = 13498.058| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.42 r_work: 0.2639 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8721 Z= 0.137 Angle : 0.868 25.984 11903 Z= 0.293 Chirality : 0.045 0.264 1238 Planarity : 0.004 0.043 1521 Dihedral : 9.400 92.879 1274 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 1.93 % Allowed : 24.40 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.26), residues: 1057 helix: 1.42 (0.30), residues: 315 sheet: 0.25 (0.44), residues: 144 loop : -0.79 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.018 0.001 TYR A 595 PHE 0.015 0.001 PHE B 106 TRP 0.010 0.001 TRP A 348 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 8701) covalent geometry : angle 0.56768 / 0.29 (11843) hydrogen bonds : bond 0.03922 / 2.67 ( 283) hydrogen bonds : angle 4.72173 / 3.42 ( 732) metal coordination : bond 0.00716 / 0.43 ( 20) metal coordination : angle 9.27182 / 6.73 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.270 Fit side-chains REVERT: A 845 MET cc_start: 0.8938 (tpt) cc_final: 0.8525 (tpt) REVERT: A 880 MET cc_start: 0.8712 (ttt) cc_final: 0.8343 (ttm) REVERT: B 50 GLU cc_start: 0.8780 (tt0) cc_final: 0.8269 (tt0) REVERT: B 120 LYS cc_start: 0.9214 (pttp) cc_final: 0.8875 (tttp) REVERT: B 133 SER cc_start: 0.7240 (t) cc_final: 0.6911 (t) REVERT: B 143 ASN cc_start: 0.9007 (t0) cc_final: 0.8699 (t0) outliers start: 17 outliers final: 13 residues processed: 97 average time/residue: 0.5998 time to fit residues: 61.8610 Evaluate side-chains 94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 52 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.061902 restraints weight = 14383.781| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.44 r_work: 0.2667 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8721 Z= 0.125 Angle : 0.852 25.543 11903 Z= 0.291 Chirality : 0.044 0.270 1238 Planarity : 0.004 0.043 1521 Dihedral : 9.300 91.787 1274 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 1.70 % Allowed : 24.74 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.27), residues: 1057 helix: 1.45 (0.30), residues: 314 sheet: 0.28 (0.44), residues: 144 loop : -0.70 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.017 0.001 TYR A 595 PHE 0.009 0.001 PHE A 475 TRP 0.009 0.001 TRP A 643 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8701) covalent geometry : angle 0.56128 / 0.29 (11843) hydrogen bonds : bond 0.03716 / 2.54 ( 283) hydrogen bonds : angle 4.64660 / 3.37 ( 732) metal coordination : bond 0.00621 / 0.37 ( 20) metal coordination : angle 9.03706 / 6.56 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.319 Fit side-chains REVERT: A 848 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8898 (mt-10) REVERT: B 32 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8210 (mp0) REVERT: B 50 GLU cc_start: 0.8845 (tt0) cc_final: 0.8251 (tt0) REVERT: B 120 LYS cc_start: 0.9279 (pttp) cc_final: 0.9040 (tttm) REVERT: B 121 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8391 (t) REVERT: B 143 ASN cc_start: 0.9110 (t0) cc_final: 0.8823 (t0) outliers start: 15 outliers final: 11 residues processed: 97 average time/residue: 0.5861 time to fit residues: 60.5205 Evaluate side-chains 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.060565 restraints weight = 13588.012| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 2.45 r_work: 0.2618 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2500 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8721 Z= 0.178 Angle : 0.886 26.985 11903 Z= 0.309 Chirality : 0.046 0.220 1238 Planarity : 0.004 0.043 1521 Dihedral : 9.439 89.753 1274 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.82 % Allowed : 24.86 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.27), residues: 1057 helix: 1.42 (0.31), residues: 314 sheet: 0.22 (0.45), residues: 143 loop : -0.78 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 38 TYR 0.019 0.001 TYR A 595 PHE 0.014 0.001 PHE B 106 TRP 0.009 0.001 TRP A 643 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 ( 8701) covalent geometry : angle 0.59822 / 0.30 (11843) hydrogen bonds : bond 0.04272 / 2.91 ( 283) hydrogen bonds : angle 4.76938 / 3.45 ( 732) metal coordination : bond 0.00928 / 0.58 ( 20) metal coordination : angle 9.23073 / 6.66 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.321 Fit side-chains REVERT: A 848 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8877 (mt-10) REVERT: B 50 GLU cc_start: 0.8755 (tt0) cc_final: 0.8132 (tt0) REVERT: B 121 CYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8328 (t) REVERT: B 143 ASN cc_start: 0.9002 (t0) cc_final: 0.8701 (t0) outliers start: 16 outliers final: 12 residues processed: 99 average time/residue: 0.6307 time to fit residues: 66.3426 Evaluate side-chains 98 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 MET Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 121 CYS Chi-restraints excluded: chain B residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.075877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.060910 restraints weight = 13695.217| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.45 r_work: 0.2627 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8721 Z= 0.162 Angle : 0.883 27.232 11903 Z= 0.307 Chirality : 0.046 0.258 1238 Planarity : 0.004 0.042 1521 Dihedral : 9.457 89.218 1274 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 1.70 % Allowed : 25.09 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.79 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.26), residues: 1057 helix: 1.41 (0.30), residues: 315 sheet: 0.24 (0.45), residues: 144 loop : -0.83 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 860 TYR 0.018 0.001 TYR A 595 PHE 0.010 0.001 PHE A 475 TRP 0.009 0.001 TRP A 643 HIS 0.005 0.001 HIS A 356 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 8701) covalent geometry : angle 0.59182 / 0.30 (11843) hydrogen bonds : bond 0.04122 / 2.80 ( 283) hydrogen bonds : angle 4.75790 / 3.43 ( 732) metal coordination : bond 0.00820 / 0.51 ( 20) metal coordination : angle 9.25411 / 6.68 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.26 seconds wall clock time: 47 minutes 57.04 seconds (2877.04 seconds total)