Starting phenix.real_space_refine on Sat May 2 21:08:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vap_64903/05_2026/9vap_64903_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vap_64903/05_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_64903/05_2026/9vap_64903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vap_64903/05_2026/9vap_64903.map" model { file = "/net/cci-nas-00/data/ceres_data/9vap_64903/05_2026/9vap_64903_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vap_64903/05_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-2.1rc2-6044/lib/python3.9/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, 104 Unusual residues: {' W': 1, 'H2S': 1, 'MGD': 2, 'SF4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 2.14, per 1000 atoms: 0.25 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: 0.90 Conformation dependent library (CDL) restraints added in 355.2 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: 0.33 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: 1.51 Time building geometry restraints manager: 1.13 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 2.540 nonbonded pdb=" S13 MGD A1101 " pdb=" W W A1105 " model vdw 2.333 2.540 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 2.540 nonbonded pdb=" SG CYS A 193 " pdb=" W W A1105 " model vdw 2.540 2.540 ... (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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.030 Find NCS groups from input model: 0.050 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:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 covalent geometry : bond 0.00297 ( 8701) covalent geometry : angle 0.55580 (11843) hydrogen bonds : bond 0.19494 ( 283) hydrogen bonds : angle 6.24360 ( 732) metal coordination : bond 0.00700 ( 20) metal coordination : angle 9.11115 ( 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 : 0.323 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: 0.6778 time to fit residues: 71.7975 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 : 0.371 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 359 ASN 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 = 0.072676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.057144 restraints weight = 16908.428| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.72 r_work: 0.2540 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2423 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.045 8721 Z= 0.362 Angle : 1.001 26.045 11903 Z= 0.362 Chirality : 0.052 0.188 1238 Planarity : 0.005 0.047 1521 Dihedral : 10.123 98.976 1289 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.85 % Rotamer: Outliers : 3.52 % Allowed : 20.54 % 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: -0.22 (0.26), residues: 1057 helix: 1.11 (0.31), residues: 315 sheet: 0.20 (0.43), residues: 151 loop : -0.95 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.025 0.002 TYR A 752 PHE 0.013 0.002 PHE A 475 TRP 0.014 0.001 TRP A 643 HIS 0.008 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00857 ( 8701) covalent geometry : angle 0.69560 (11843) hydrogen bonds : bond 0.06201 ( 283) hydrogen bonds : angle 5.38527 ( 732) metal coordination : bond 0.01887 ( 20) metal coordination : angle 10.15482 ( 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 : 0.323 Fit side-chains REVERT: A 845 MET cc_start: 0.8892 (tpt) cc_final: 0.8482 (tpt) REVERT: A 848 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9040 (mt-10) REVERT: B 9 ASP cc_start: 0.8883 (t0) cc_final: 0.8682 (t0) REVERT: B 32 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8392 (mm-30) REVERT: B 168 GLU cc_start: 0.8308 (pp20) cc_final: 0.7996 (tm-30) outliers start: 31 outliers final: 16 residues processed: 102 average time/residue: 0.6880 time to fit residues: 74.2821 Evaluate side-chains 98 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 0.8980 chunk 95 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3055 r_free = 0.3055 target = 0.077142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.061605 restraints weight = 16342.126| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.74 r_work: 0.2635 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.0687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8721 Z= 0.098 Angle : 0.840 22.819 11903 Z= 0.270 Chirality : 0.043 0.159 1238 Planarity : 0.004 0.046 1521 Dihedral : 9.440 100.966 1277 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.88 % Favored : 96.03 % Rotamer: Outliers : 2.38 % Allowed : 22.36 % Favored : 75.26 % 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: -0.00 (0.26), residues: 1057 helix: 1.35 (0.31), residues: 316 sheet: 0.32 (0.44), residues: 143 loop : -0.84 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 860 TYR 0.015 0.001 TYR A 595 PHE 0.009 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 covalent geometry : bond 0.00216 ( 8701) covalent geometry : angle 0.51288 (11843) hydrogen bonds : bond 0.03833 ( 283) hydrogen bonds : angle 4.87471 ( 732) metal coordination : bond 0.00548 ( 20) metal coordination : angle 9.37554 ( 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 108 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.324 Fit side-chains REVERT: A 699 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: A 845 MET cc_start: 0.8954 (tpt) cc_final: 0.8573 (tpt) REVERT: B 32 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8163 (mm-30) REVERT: B 50 GLU cc_start: 0.8773 (tt0) cc_final: 0.8142 (tt0) REVERT: B 105 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: B 121 CYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8136 (t) REVERT: B 155 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7301 (mp0) outliers start: 21 outliers final: 7 residues processed: 99 average time/residue: 0.7037 time to fit residues: 73.7130 Evaluate side-chains 94 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 699 GLN Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 936 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: 3.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 0.0010 chunk 83 optimal weight: 7.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.060034 restraints weight = 16551.332| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 2.71 r_work: 0.2593 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8721 Z= 0.175 Angle : 0.866 23.174 11903 Z= 0.290 Chirality : 0.045 0.151 1238 Planarity : 0.004 0.045 1521 Dihedral : 9.457 96.831 1274 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 2.27 % Allowed : 22.93 % 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 (0.27), residues: 1057 helix: 1.40 (0.31), residues: 315 sheet: 0.22 (0.46), residues: 134 loop : -0.76 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 38 TYR 0.019 0.001 TYR A 595 PHE 0.011 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 covalent geometry : bond 0.00415 ( 8701) covalent geometry : angle 0.55998 (11843) hydrogen bonds : bond 0.04360 ( 283) hydrogen bonds : angle 4.85580 ( 732) metal coordination : bond 0.00955 ( 20) metal coordination : angle 9.32334 ( 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 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.382 Fit side-chains REVERT: A 845 MET cc_start: 0.8922 (tpt) cc_final: 0.8478 (tpt) REVERT: B 32 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8268 (mm-30) REVERT: B 50 GLU cc_start: 0.8700 (tt0) cc_final: 0.8218 (tt0) REVERT: B 121 CYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8160 (t) REVERT: B 168 GLU cc_start: 0.8308 (pp20) cc_final: 0.7920 (tm-30) outliers start: 20 outliers final: 14 residues processed: 98 average time/residue: 0.7273 time to fit residues: 75.2427 Evaluate side-chains 96 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 800 LEU Chi-restraints excluded: chain A residue 926 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 16 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 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: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.073536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.057981 restraints weight = 16902.621| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 2.74 r_work: 0.2552 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 8721 Z= 0.299 Angle : 0.953 26.335 11903 Z= 0.336 Chirality : 0.050 0.174 1238 Planarity : 0.004 0.047 1521 Dihedral : 9.782 93.600 1274 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.96 % Favored : 93.95 % Rotamer: Outliers : 3.41 % Allowed : 22.25 % Favored : 74.35 % 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: -0.19 (0.26), residues: 1057 helix: 1.25 (0.30), residues: 317 sheet: 0.15 (0.44), residues: 151 loop : -0.99 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 38 TYR 0.023 0.002 TYR A 595 PHE 0.013 0.001 PHE A 475 TRP 0.012 0.001 TRP A 643 HIS 0.007 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 8701) covalent geometry : angle 0.64853 (11843) hydrogen bonds : bond 0.05457 ( 283) hydrogen bonds : angle 5.12358 ( 732) metal coordination : bond 0.01507 ( 20) metal coordination : angle 9.86387 ( 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 114 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.334 Fit side-chains REVERT: A 845 MET cc_start: 0.8918 (tpt) cc_final: 0.8505 (tpt) REVERT: B 32 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8328 (mm-30) REVERT: B 50 GLU cc_start: 0.8649 (tt0) cc_final: 0.8144 (tt0) REVERT: B 120 LYS cc_start: 0.9110 (pttp) cc_final: 0.8615 (tttp) REVERT: B 121 CYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8309 (t) REVERT: B 143 ASN cc_start: 0.8990 (t0) cc_final: 0.8691 (t0) REVERT: B 155 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7490 (mp0) REVERT: B 168 GLU cc_start: 0.8326 (pp20) cc_final: 0.7937 (tm-30) outliers start: 30 outliers final: 19 residues processed: 103 average time/residue: 0.6903 time to fit residues: 75.1882 Evaluate side-chains 103 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 818 THR 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 42 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 76 ARG 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: 0.0010 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 103 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.077489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.062434 restraints weight = 15235.114| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.54 r_work: 0.2693 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8721 Z= 0.093 Angle : 0.824 23.761 11903 Z= 0.266 Chirality : 0.042 0.141 1238 Planarity : 0.004 0.046 1521 Dihedral : 9.291 92.207 1274 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.35 % Favored : 95.55 % Rotamer: Outliers : 2.04 % Allowed : 23.38 % Favored : 74.57 % 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: 1.40 (0.30), residues: 315 sheet: 0.22 (0.46), residues: 134 loop : -0.71 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 418 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8701) covalent geometry : angle 0.51137 (11843) hydrogen bonds : bond 0.03246 ( 283) hydrogen bonds : angle 4.66260 ( 732) metal coordination : bond 0.00446 ( 20) metal coordination : angle 9.11606 ( 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 106 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.344 Fit side-chains REVERT: A 845 MET cc_start: 0.9038 (tpt) cc_final: 0.8660 (tpt) REVERT: A 848 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8825 (mt-10) REVERT: B 32 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8249 (mm-30) REVERT: B 50 GLU cc_start: 0.8836 (tt0) cc_final: 0.8271 (tt0) REVERT: B 143 ASN cc_start: 0.9090 (t0) cc_final: 0.8799 (t0) REVERT: B 155 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7637 (mt-10) outliers start: 18 outliers final: 6 residues processed: 102 average time/residue: 0.6856 time to fit residues: 74.0743 Evaluate side-chains 90 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 934 THR 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: 6.9990 chunk 65 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 15 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.073309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.057790 restraints weight = 16879.441| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 2.74 r_work: 0.2558 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 8721 Z= 0.300 Angle : 0.957 27.563 11903 Z= 0.341 Chirality : 0.050 0.171 1238 Planarity : 0.005 0.046 1521 Dihedral : 9.820 91.305 1274 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.43 % Favored : 93.47 % Rotamer: Outliers : 2.50 % Allowed : 23.16 % Favored : 74.35 % 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: -0.15 (0.26), residues: 1057 helix: 1.28 (0.30), residues: 317 sheet: 0.17 (0.44), residues: 151 loop : -0.97 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 38 TYR 0.024 0.002 TYR A 595 PHE 0.013 0.001 PHE A 475 TRP 0.011 0.001 TRP A 643 HIS 0.007 0.001 HIS A 559 Details of bonding type rmsd covalent geometry : bond 0.00708 ( 8701) covalent geometry : angle 0.66006 (11843) hydrogen bonds : bond 0.05400 ( 283) hydrogen bonds : angle 5.02620 ( 732) metal coordination : bond 0.01570 ( 20) metal coordination : angle 9.78542 ( 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 105 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.334 Fit side-chains REVERT: A 845 MET cc_start: 0.8912 (tpt) cc_final: 0.8496 (tpt) REVERT: A 848 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8819 (mt-10) REVERT: B 32 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8143 (mp0) REVERT: B 50 GLU cc_start: 0.8667 (tt0) cc_final: 0.8114 (tt0) REVERT: B 121 CYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8284 (t) REVERT: B 143 ASN cc_start: 0.8959 (t0) cc_final: 0.8692 (t0) REVERT: B 166 ASP cc_start: 0.7786 (p0) cc_final: 0.7509 (p0) outliers start: 22 outliers final: 14 residues processed: 101 average time/residue: 0.6739 time to fit residues: 72.2457 Evaluate side-chains 99 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 936 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 0.0020 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 = 0.3051 r_free = 0.3051 target = 0.076461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.061166 restraints weight = 16092.497| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.71 r_work: 0.2641 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8721 Z= 0.107 Angle : 0.862 25.764 11903 Z= 0.289 Chirality : 0.044 0.238 1238 Planarity : 0.004 0.046 1521 Dihedral : 9.513 90.207 1274 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.07 % Favored : 95.84 % Rotamer: Outliers : 1.82 % Allowed : 24.06 % Favored : 74.12 % 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 (0.27), residues: 1057 helix: 1.40 (0.31), residues: 314 sheet: 0.25 (0.44), residues: 144 loop : -0.77 (0.26), residues: 599 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 0.016 0.001 PHE B 106 TRP 0.009 0.001 TRP A 348 HIS 0.004 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8701) covalent geometry : angle 0.55728 (11843) hydrogen bonds : bond 0.03662 ( 283) hydrogen bonds : angle 4.73457 ( 732) metal coordination : bond 0.00527 ( 20) metal coordination : angle 9.28068 ( 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 103 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.323 Fit side-chains REVERT: A 848 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8724 (mt-10) REVERT: B 32 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8225 (mm-30) REVERT: B 50 GLU cc_start: 0.8739 (tt0) cc_final: 0.8199 (tt0) REVERT: B 133 SER cc_start: 0.7255 (t) cc_final: 0.6819 (t) REVERT: B 143 ASN cc_start: 0.8902 (t0) cc_final: 0.8621 (t0) outliers start: 16 outliers final: 9 residues processed: 99 average time/residue: 0.6543 time to fit residues: 68.7891 Evaluate side-chains 93 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 531 THR 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 B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL 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: 0.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 26 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3086 r_free = 0.3086 target = 0.077552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.062682 restraints weight = 14819.572| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.49 r_work: 0.2698 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.002 0.039 8721 Z= 0.102 Angle : 0.835 24.262 11903 Z= 0.284 Chirality : 0.043 0.230 1238 Planarity : 0.004 0.044 1521 Dihedral : 9.225 88.502 1274 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.64 % Favored : 95.27 % Rotamer: Outliers : 1.48 % Allowed : 24.18 % Favored : 74.35 % 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: 0.16 (0.27), residues: 1057 helix: 1.48 (0.31), residues: 314 sheet: 0.29 (0.44), residues: 144 loop : -0.68 (0.26), residues: 599 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 0.007 0.001 PHE A 475 TRP 0.008 0.001 TRP A 643 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8701) covalent geometry : angle 0.54811 (11843) hydrogen bonds : bond 0.03359 ( 283) hydrogen bonds : angle 4.57901 ( 732) metal coordination : bond 0.00506 ( 20) metal coordination : angle 8.89208 ( 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 102 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.311 Fit side-chains REVERT: A 848 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8851 (mt-10) REVERT: B 32 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8171 (mp0) REVERT: B 50 GLU cc_start: 0.8843 (tt0) cc_final: 0.8345 (tt0) REVERT: B 120 LYS cc_start: 0.9310 (pttp) cc_final: 0.9009 (tttp) REVERT: B 143 ASN cc_start: 0.9116 (t0) cc_final: 0.8858 (t0) REVERT: B 166 ASP cc_start: 0.7619 (p0) cc_final: 0.6988 (p0) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.6296 time to fit residues: 66.0194 Evaluate side-chains 95 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 531 THR 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 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: 4.9990 chunk 73 optimal weight: 0.2980 chunk 54 optimal weight: 5.9990 chunk 102 optimal weight: 0.0170 chunk 49 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.079252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.064317 restraints weight = 15063.611| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.53 r_work: 0.2733 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8721 Z= 0.093 Angle : 0.822 24.380 11903 Z= 0.282 Chirality : 0.043 0.309 1238 Planarity : 0.004 0.043 1521 Dihedral : 9.027 87.246 1274 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % Rotamer: Outliers : 0.91 % Allowed : 24.52 % Favored : 74.57 % 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: 0.28 (0.27), residues: 1057 helix: 1.54 (0.30), residues: 314 sheet: 0.44 (0.44), residues: 143 loop : -0.61 (0.26), residues: 600 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 0.008 0.001 TRP A 418 HIS 0.002 0.000 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8701) covalent geometry : angle 0.54399 (11843) hydrogen bonds : bond 0.03054 ( 283) hydrogen bonds : angle 4.48831 ( 732) metal coordination : bond 0.00388 ( 20) metal coordination : angle 8.69491 ( 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 97 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.403 Fit side-chains REVERT: A 845 MET cc_start: 0.8954 (tpt) cc_final: 0.8547 (tpt) REVERT: B 50 GLU cc_start: 0.8814 (tt0) cc_final: 0.8313 (tt0) REVERT: B 120 LYS cc_start: 0.9334 (pttp) cc_final: 0.9085 (tttp) REVERT: B 143 ASN cc_start: 0.9107 (t0) cc_final: 0.8894 (t0) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.6511 time to fit residues: 65.7971 Evaluate side-chains 92 residues out of total 881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 800 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain B residue 60 CYS Chi-restraints excluded: chain B residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 63 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3116 r_free = 0.3116 target = 0.078975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.064042 restraints weight = 15292.380| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.58 r_work: 0.2725 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8721 Z= 0.106 Angle : 0.818 24.413 11903 Z= 0.282 Chirality : 0.043 0.134 1238 Planarity : 0.004 0.043 1521 Dihedral : 8.969 86.223 1274 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.11 % Favored : 94.80 % Rotamer: Outliers : 0.79 % Allowed : 25.43 % Favored : 73.78 % 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: 0.25 (0.27), residues: 1057 helix: 1.54 (0.30), residues: 316 sheet: 0.41 (0.44), residues: 144 loop : -0.65 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 175 TYR 0.016 0.001 TYR A 595 PHE 0.010 0.001 PHE B 132 TRP 0.008 0.001 TRP A 643 HIS 0.003 0.001 HIS A 356 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8701) covalent geometry : angle 0.54725 (11843) hydrogen bonds : bond 0.03136 ( 283) hydrogen bonds : angle 4.47995 ( 732) metal coordination : bond 0.00510 ( 20) metal coordination : angle 8.57555 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2816.06 seconds wall clock time: 48 minutes 53.13 seconds (2933.13 seconds total)