Starting phenix.real_space_refine on Thu May 22 17:58:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.map" model { file = "/net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9he1_52074/05_2025/9he1_52074.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 7460 2.51 5 N 2023 2.21 5 O 2322 1.98 5 H 11404 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23241 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 12141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 786, 12141 Classifications: {'peptide': 786} Link IDs: {'PTRANS': 29, 'TRANS': 756} Chain: "B" Number of atoms: 5416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5416 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 1 Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 844 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 6, 'TRANS': 51} Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3346 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 12, 'TRANS': 196} Chain breaks: 1 Chain: "E" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1291 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "G" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 203 Classifications: {'peptide': 12} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 11} Time building chain proxies: 11.21, per 1000 atoms: 0.48 Number of scatterers: 23241 At special positions: 0 Unit cell: (139.656, 122.958, 137.379, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2322 8.00 N 2023 7.00 C 7460 6.00 H 11404 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 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: 5.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2766 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 17 sheets defined 23.4% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 69 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.837A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 233 removed outlier: 3.668A pdb=" N ARG A 233 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 4.462A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU A 287 " --> pdb=" O GLU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 314 removed outlier: 3.627A pdb=" N VAL A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.917A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.096A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.848A pdb=" N GLY A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 removed outlier: 3.712A pdb=" N TRP A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 730 removed outlier: 3.574A pdb=" N TYR A 729 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 730 " --> pdb=" O ASP A 727 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 726 through 730' Processing helix chain 'C' and resid 32 through 39 removed outlier: 3.957A pdb=" N SER C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 39' Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.754A pdb=" N ILE D 52 " --> pdb=" O TRP D 48 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 105 through 121 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 removed outlier: 3.588A pdb=" N PHE D 169 " --> pdb=" O LYS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.684A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.691A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 Processing helix chain 'D' and resid 227 through 240 Processing helix chain 'E' and resid 41 through 45 Processing helix chain 'E' and resid 51 through 59 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.470A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU A 32 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU A 90 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 4.413A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 183 removed outlier: 7.822A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 193 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 removed outlier: 4.180A pdb=" N GLU A 294 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 270 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 341 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 343 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 355 removed outlier: 7.792A pdb=" N VAL A 414 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE A 352 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR A 416 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE A 354 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL A 418 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 802 through 805 removed outlier: 3.893A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 636 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 590 " --> pdb=" O TYR A 618 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.894A pdb=" N ALA A 672 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 44 through 50 removed outlier: 4.647A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP B 48 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 67 removed outlier: 6.781A pdb=" N VAL B 81 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER B 94 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.066A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.471A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 201 through 203 removed outlier: 6.535A pdb=" N VAL B 216 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLN B 229 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 218 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 252 through 254 removed outlier: 4.001A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.744A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 331 through 333 removed outlier: 5.654A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.664A pdb=" N PHE E 74 " --> pdb=" O MET E 64 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 32 through 35 536 hydrogen bonds defined for protein. 1500 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: 9.16 Time building geometry restraints manager: 6.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11404 1.03 - 1.23: 1 1.23 - 1.42: 5238 1.42 - 1.62: 6796 1.62 - 1.81: 62 Bond restraints: 23501 Sorted by residual: bond pdb=" N LYS A 798 " pdb=" CA LYS A 798 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.14e-02 7.69e+03 6.92e+00 bond pdb=" N ASP A 797 " pdb=" CA ASP A 797 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.33e-02 5.65e+03 6.38e+00 bond pdb=" N GLY A 796 " pdb=" H GLY A 796 " ideal model delta sigma weight residual 0.860 0.907 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" N ASP D 134 " pdb=" CA ASP D 134 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.32e-02 5.74e+03 5.12e+00 bond pdb=" N GLY A 796 " pdb=" CA GLY A 796 " ideal model delta sigma weight residual 1.448 1.477 -0.030 1.40e-02 5.10e+03 4.50e+00 ... (remaining 23496 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 39103 0.91 - 1.82: 2965 1.82 - 2.73: 128 2.73 - 3.64: 53 3.64 - 4.55: 12 Bond angle restraints: 42261 Sorted by residual: angle pdb=" CA ASP D 134 " pdb=" CB ASP D 134 " pdb=" CG ASP D 134 " ideal model delta sigma weight residual 112.60 116.38 -3.78 1.00e+00 1.00e+00 1.43e+01 angle pdb=" CA LYS A 798 " pdb=" C LYS A 798 " pdb=" O LYS A 798 " ideal model delta sigma weight residual 121.67 117.25 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA ASP A 797 " pdb=" CB ASP A 797 " pdb=" CG ASP A 797 " ideal model delta sigma weight residual 112.60 115.88 -3.28 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA ASP A 797 " pdb=" C ASP A 797 " pdb=" O ASP A 797 " ideal model delta sigma weight residual 120.92 117.95 2.97 1.15e+00 7.56e-01 6.67e+00 angle pdb=" C GLY B 53 " pdb=" N SER B 54 " pdb=" CA SER B 54 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.68e+00 ... (remaining 42256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 10445 15.82 - 31.65: 474 31.65 - 47.47: 147 47.47 - 63.29: 75 63.29 - 79.12: 3 Dihedral angle restraints: 11144 sinusoidal: 5995 harmonic: 5149 Sorted by residual: dihedral pdb=" CA GLN A 495 " pdb=" CB GLN A 495 " pdb=" CG GLN A 495 " pdb=" CD GLN A 495 " ideal model delta sinusoidal sigma weight residual 60.00 118.08 -58.08 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG D 166 " pdb=" CB ARG D 166 " pdb=" CG ARG D 166 " pdb=" CD ARG D 166 " ideal model delta sinusoidal sigma weight residual -60.00 -117.97 57.97 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N CYS A 690 " pdb=" CA CYS A 690 " pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " ideal model delta sinusoidal sigma weight residual -180.00 -125.88 -54.12 3 1.50e+01 4.44e-03 9.26e+00 ... (remaining 11141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1073 0.028 - 0.055: 474 0.055 - 0.083: 94 0.083 - 0.111: 101 0.111 - 0.139: 45 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CA LYS A 798 " pdb=" N LYS A 798 " pdb=" C LYS A 798 " pdb=" CB LYS A 798 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE B 164 " pdb=" N ILE B 164 " pdb=" C ILE B 164 " pdb=" CB ILE B 164 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1784 not shown) Planarity restraints: 3603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 7 " 0.115 9.50e-02 1.11e+02 3.84e-02 1.62e+00 pdb=" NE ARG G 7 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG G 7 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG G 7 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 7 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 7 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG G 7 " -0.001 2.00e-02 2.50e+03 pdb="HH21 ARG G 7 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG G 7 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 1 " 0.012 2.00e-02 2.50e+03 6.08e-03 1.39e+00 pdb=" CG TRP G 1 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP G 1 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP G 1 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 1 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 1 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 1 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 1 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 1 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP G 1 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP G 1 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP G 1 " -0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP G 1 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 1 " -0.002 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 154 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO B 155 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 155 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 155 " 0.016 5.00e-02 4.00e+02 ... (remaining 3600 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 132 2.01 - 2.66: 31411 2.66 - 3.31: 63886 3.31 - 3.95: 80717 3.95 - 4.60: 126828 Nonbonded interactions: 302974 Sorted by model distance: nonbonded pdb=" CH2 TRP G 1 " pdb=" HB3 ASN G 3 " model vdw 1.365 2.970 nonbonded pdb=" CE2 PHE G 5 " pdb=" CB ARG G 7 " model vdw 1.521 3.450 nonbonded pdb=" CH2 TRP G 8 " pdb=" CB LYS G 10 " model vdw 1.522 3.450 nonbonded pdb=" CH2 TRP G 1 " pdb=" CB ASN G 3 " model vdw 1.537 3.450 nonbonded pdb=" CH2 TRP G 8 " pdb=" HB3 LYS G 10 " model vdw 1.626 2.970 ... (remaining 302969 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: 5.430 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: 0.390 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 49.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12098 Z= 0.098 Angle : 0.425 4.552 16442 Z= 0.236 Chirality : 0.041 0.139 1787 Planarity : 0.003 0.050 2164 Dihedral : 8.803 65.374 4377 Min Nonbonded Distance : 1.521 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.39 % Allowed : 2.76 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.22), residues: 1495 helix: 3.19 (0.29), residues: 309 sheet: 0.40 (0.23), residues: 456 loop : -0.81 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 1 HIS 0.001 0.000 HIS D 139 PHE 0.009 0.001 PHE E 77 TYR 0.010 0.001 TYR D 184 ARG 0.001 0.000 ARG A 353 Details of bonding type rmsd hydrogen bonds : bond 0.11943 ( 532) hydrogen bonds : angle 4.83335 ( 1500) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.08855 ( 2) covalent geometry : bond 0.00189 (12097) covalent geometry : angle 0.42505 (16440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8629 (ttp) cc_final: 0.8400 (tpp) REVERT: B 60 TYR cc_start: 0.6365 (t80) cc_final: 0.6161 (t80) REVERT: B 123 TYR cc_start: 0.4900 (m-80) cc_final: 0.4505 (m-80) REVERT: B 143 TRP cc_start: 0.3671 (p-90) cc_final: 0.2846 (p-90) REVERT: B 226 MET cc_start: 0.5497 (tmm) cc_final: 0.4910 (ppp) outliers start: 5 outliers final: 0 residues processed: 137 average time/residue: 2.3799 time to fit residues: 356.7014 Evaluate side-chains 88 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN A 606 ASN B 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.219761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.137317 restraints weight = 55800.563| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.84 r_work: 0.3646 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12098 Z= 0.120 Angle : 0.463 4.149 16442 Z= 0.249 Chirality : 0.042 0.140 1787 Planarity : 0.004 0.037 2164 Dihedral : 3.523 16.295 1656 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.95 % Allowed : 6.71 % Favored : 92.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1495 helix: 2.83 (0.29), residues: 311 sheet: 0.26 (0.23), residues: 471 loop : -0.96 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 1 HIS 0.003 0.000 HIS B 121 PHE 0.019 0.001 PHE A 426 TYR 0.013 0.001 TYR C 41 ARG 0.004 0.000 ARG A 592 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 532) hydrogen bonds : angle 4.43884 ( 1500) SS BOND : bond 0.00217 ( 1) SS BOND : angle 1.03214 ( 2) covalent geometry : bond 0.00269 (12097) covalent geometry : angle 0.46280 (16440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8637 (ttp) cc_final: 0.8424 (tpp) REVERT: A 746 ASP cc_start: 0.8009 (t0) cc_final: 0.7702 (p0) REVERT: A 774 LEU cc_start: 0.7738 (pp) cc_final: 0.7166 (mp) REVERT: B 60 TYR cc_start: 0.6377 (t80) cc_final: 0.6160 (t80) REVERT: B 123 TYR cc_start: 0.4861 (m-80) cc_final: 0.4558 (m-80) REVERT: B 226 MET cc_start: 0.5527 (tmm) cc_final: 0.4934 (ppp) REVERT: E 53 GLN cc_start: 0.7795 (mm-40) cc_final: 0.7413 (tp-100) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 2.2258 time to fit residues: 263.7210 Evaluate side-chains 92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 131 optimal weight: 0.1980 chunk 102 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 119 optimal weight: 0.1980 chunk 128 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4723 r_free = 0.4723 target = 0.219352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136870 restraints weight = 55695.525| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.81 r_work: 0.3622 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12098 Z= 0.105 Angle : 0.447 4.358 16442 Z= 0.241 Chirality : 0.042 0.135 1787 Planarity : 0.003 0.031 2164 Dihedral : 3.554 15.904 1656 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.63 % Allowed : 7.42 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1495 helix: 2.83 (0.29), residues: 311 sheet: 0.25 (0.23), residues: 473 loop : -1.00 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 8 HIS 0.003 0.000 HIS B 121 PHE 0.017 0.001 PHE G 5 TYR 0.014 0.001 TYR A 465 ARG 0.004 0.000 ARG G 7 Details of bonding type rmsd hydrogen bonds : bond 0.03892 ( 532) hydrogen bonds : angle 4.37105 ( 1500) SS BOND : bond 0.01748 ( 1) SS BOND : angle 3.05788 ( 2) covalent geometry : bond 0.00233 (12097) covalent geometry : angle 0.44618 (16440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 MET cc_start: 0.8667 (ttp) cc_final: 0.8460 (tpp) REVERT: A 736 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7593 (t) REVERT: A 746 ASP cc_start: 0.8026 (t0) cc_final: 0.7684 (p0) REVERT: A 776 TRP cc_start: 0.7590 (t60) cc_final: 0.7374 (t60) REVERT: B 60 TYR cc_start: 0.6359 (t80) cc_final: 0.6138 (t80) REVERT: B 123 TYR cc_start: 0.4818 (m-80) cc_final: 0.4522 (m-80) REVERT: B 226 MET cc_start: 0.5461 (tmm) cc_final: 0.4920 (pmm) REVERT: E 53 GLN cc_start: 0.7834 (mm-40) cc_final: 0.7450 (tp-100) outliers start: 8 outliers final: 4 residues processed: 97 average time/residue: 2.1618 time to fit residues: 231.5985 Evaluate side-chains 92 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 98 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.215174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.131120 restraints weight = 55027.940| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.68 r_work: 0.3536 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12098 Z= 0.178 Angle : 0.519 4.841 16442 Z= 0.285 Chirality : 0.043 0.141 1787 Planarity : 0.004 0.035 2164 Dihedral : 3.937 20.636 1656 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.10 % Allowed : 7.10 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.22), residues: 1495 helix: 2.28 (0.29), residues: 311 sheet: 0.10 (0.23), residues: 474 loop : -1.19 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 1 HIS 0.006 0.001 HIS D 139 PHE 0.020 0.002 PHE E 77 TYR 0.019 0.002 TYR D 62 ARG 0.004 0.000 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 532) hydrogen bonds : angle 4.66296 ( 1500) SS BOND : bond 0.01525 ( 1) SS BOND : angle 1.02000 ( 2) covalent geometry : bond 0.00421 (12097) covalent geometry : angle 0.51851 (16440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 TYR cc_start: 0.6290 (t80) cc_final: 0.6080 (t80) REVERT: B 123 TYR cc_start: 0.4825 (m-80) cc_final: 0.4569 (m-80) REVERT: B 226 MET cc_start: 0.5432 (tmm) cc_final: 0.4789 (pmm) REVERT: C 41 TYR cc_start: 0.7759 (p90) cc_final: 0.5519 (t80) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 2.1068 time to fit residues: 220.0230 Evaluate side-chains 84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 56 GLU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 142 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 109 optimal weight: 50.0000 chunk 125 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.217347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134574 restraints weight = 55411.821| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.75 r_work: 0.3586 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12098 Z= 0.094 Angle : 0.459 8.443 16442 Z= 0.246 Chirality : 0.042 0.136 1787 Planarity : 0.003 0.039 2164 Dihedral : 3.717 17.210 1656 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.71 % Allowed : 8.21 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1495 helix: 2.67 (0.29), residues: 311 sheet: 0.16 (0.23), residues: 472 loop : -1.12 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.003 0.000 HIS B 121 PHE 0.010 0.001 PHE E 77 TYR 0.016 0.001 TYR A 465 ARG 0.002 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 532) hydrogen bonds : angle 4.40505 ( 1500) SS BOND : bond 0.00229 ( 1) SS BOND : angle 3.19101 ( 2) covalent geometry : bond 0.00196 (12097) covalent geometry : angle 0.45791 (16440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 774 LEU cc_start: 0.7824 (pp) cc_final: 0.7247 (mp) REVERT: B 60 TYR cc_start: 0.6272 (t80) cc_final: 0.6068 (t80) REVERT: B 123 TYR cc_start: 0.4804 (m-80) cc_final: 0.4507 (m-80) REVERT: B 226 MET cc_start: 0.5355 (tmm) cc_final: 0.4771 (pmm) REVERT: C 41 TYR cc_start: 0.7635 (p90) cc_final: 0.5484 (t80) REVERT: C 56 MET cc_start: 0.7754 (ptm) cc_final: 0.7535 (ptp) REVERT: E 53 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7434 (tp-100) outliers start: 9 outliers final: 6 residues processed: 87 average time/residue: 1.9872 time to fit residues: 194.2373 Evaluate side-chains 83 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 49 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 141 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.4702 r_free = 0.4702 target = 0.217024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.133483 restraints weight = 55136.152| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.83 r_work: 0.3577 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12098 Z= 0.110 Angle : 0.461 9.268 16442 Z= 0.247 Chirality : 0.042 0.136 1787 Planarity : 0.004 0.041 2164 Dihedral : 3.693 16.635 1656 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.63 % Allowed : 8.84 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1495 helix: 2.67 (0.29), residues: 311 sheet: 0.22 (0.23), residues: 466 loop : -1.15 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 1 HIS 0.003 0.001 HIS A 533 PHE 0.011 0.001 PHE E 77 TYR 0.016 0.001 TYR A 465 ARG 0.002 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 532) hydrogen bonds : angle 4.37099 ( 1500) SS BOND : bond 0.00598 ( 1) SS BOND : angle 1.58714 ( 2) covalent geometry : bond 0.00249 (12097) covalent geometry : angle 0.46044 (16440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 TYR cc_start: 0.6304 (t80) cc_final: 0.6098 (t80) REVERT: B 123 TYR cc_start: 0.4794 (m-80) cc_final: 0.4507 (m-80) REVERT: B 226 MET cc_start: 0.5406 (tmm) cc_final: 0.4855 (pmm) REVERT: C 41 TYR cc_start: 0.7706 (p90) cc_final: 0.5446 (t80) REVERT: E 53 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7482 (tp-100) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 2.0084 time to fit residues: 188.7260 Evaluate side-chains 81 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 30.0000 chunk 14 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 130 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 83 optimal weight: 40.0000 chunk 131 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 10 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 555 HIS A 693 GLN D 99 ASN D 196 ASN E 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.211542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127863 restraints weight = 54881.349| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 4.44 r_work: 0.3401 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 12098 Z= 0.332 Angle : 0.660 7.370 16442 Z= 0.367 Chirality : 0.048 0.226 1787 Planarity : 0.005 0.047 2164 Dihedral : 4.546 27.016 1656 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 1.58 % Allowed : 8.84 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.21), residues: 1495 helix: 1.44 (0.29), residues: 311 sheet: -0.01 (0.23), residues: 452 loop : -1.52 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 635 HIS 0.012 0.002 HIS A 533 PHE 0.026 0.002 PHE E 77 TYR 0.031 0.002 TYR D 62 ARG 0.008 0.001 ARG D 197 Details of bonding type rmsd hydrogen bonds : bond 0.06793 ( 532) hydrogen bonds : angle 5.13087 ( 1500) SS BOND : bond 0.00911 ( 1) SS BOND : angle 1.74768 ( 2) covalent geometry : bond 0.00802 (12097) covalent geometry : angle 0.66015 (16440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 757 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: A 783 LEU cc_start: 0.7876 (tt) cc_final: 0.7661 (mp) REVERT: B 60 TYR cc_start: 0.6295 (t80) cc_final: 0.6030 (t80) REVERT: B 123 TYR cc_start: 0.4743 (m-80) cc_final: 0.4509 (m-80) REVERT: B 226 MET cc_start: 0.5441 (tmm) cc_final: 0.4884 (pmm) REVERT: C 41 TYR cc_start: 0.7927 (p90) cc_final: 0.5490 (t80) REVERT: D 48 TRP cc_start: 0.5792 (m100) cc_final: 0.4159 (m-90) outliers start: 20 outliers final: 11 residues processed: 100 average time/residue: 1.9571 time to fit residues: 218.9563 Evaluate side-chains 89 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 736 SER Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 797 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 10.0000 chunk 68 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN D 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.215196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134479 restraints weight = 55258.305| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 4.00 r_work: 0.3526 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12098 Z= 0.119 Angle : 0.504 8.681 16442 Z= 0.271 Chirality : 0.043 0.137 1787 Planarity : 0.004 0.065 2164 Dihedral : 4.057 18.398 1656 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.63 % Allowed : 10.26 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1495 helix: 2.15 (0.29), residues: 310 sheet: -0.00 (0.23), residues: 467 loop : -1.43 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 749 HIS 0.003 0.001 HIS B 121 PHE 0.012 0.001 PHE E 77 TYR 0.017 0.001 TYR A 465 ARG 0.007 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 532) hydrogen bonds : angle 4.63464 ( 1500) SS BOND : bond 0.00261 ( 1) SS BOND : angle 5.36548 ( 2) covalent geometry : bond 0.00261 (12097) covalent geometry : angle 0.50069 (16440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.7527 (pp30) cc_final: 0.7005 (pp30) REVERT: B 60 TYR cc_start: 0.6347 (t80) cc_final: 0.6094 (t80) REVERT: B 123 TYR cc_start: 0.4803 (m-80) cc_final: 0.4513 (m-80) REVERT: B 226 MET cc_start: 0.5436 (tmm) cc_final: 0.4726 (ppp) REVERT: C 41 TYR cc_start: 0.7641 (p90) cc_final: 0.5381 (t80) REVERT: D 48 TRP cc_start: 0.5122 (m100) cc_final: 0.3692 (m-90) REVERT: D 58 LEU cc_start: 0.6346 (tm) cc_final: 0.6134 (tt) REVERT: D 112 ARG cc_start: 0.7377 (ttt-90) cc_final: 0.7142 (ttt-90) REVERT: E 53 GLN cc_start: 0.7722 (mm-40) cc_final: 0.7400 (tp-100) REVERT: G 2 VAL cc_start: 0.9169 (t) cc_final: 0.8909 (p) outliers start: 8 outliers final: 5 residues processed: 89 average time/residue: 2.0827 time to fit residues: 205.9676 Evaluate side-chains 84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain E residue 31 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 118 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 137 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 5 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- 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 = 0.4695 r_free = 0.4695 target = 0.215179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.134208 restraints weight = 54951.653| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.04 r_work: 0.3517 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12098 Z= 0.115 Angle : 0.494 9.696 16442 Z= 0.263 Chirality : 0.042 0.134 1787 Planarity : 0.004 0.077 2164 Dihedral : 3.974 17.962 1656 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.63 % Allowed : 10.18 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.22), residues: 1495 helix: 2.34 (0.29), residues: 310 sheet: -0.02 (0.22), residues: 474 loop : -1.41 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.003 0.001 HIS A 533 PHE 0.016 0.001 PHE A 440 TYR 0.016 0.001 TYR A 465 ARG 0.008 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.04224 ( 532) hydrogen bonds : angle 4.56405 ( 1500) SS BOND : bond 0.00772 ( 1) SS BOND : angle 3.71305 ( 2) covalent geometry : bond 0.00256 (12097) covalent geometry : angle 0.49200 (16440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 TYR cc_start: 0.6354 (t80) cc_final: 0.6110 (t80) REVERT: B 123 TYR cc_start: 0.4776 (m-80) cc_final: 0.4496 (m-80) REVERT: B 226 MET cc_start: 0.5443 (tmm) cc_final: 0.4749 (ppp) REVERT: C 41 TYR cc_start: 0.7688 (p90) cc_final: 0.5385 (t80) REVERT: D 48 TRP cc_start: 0.5208 (m100) cc_final: 0.3746 (m-90) REVERT: D 58 LEU cc_start: 0.6116 (tm) cc_final: 0.5886 (tt) REVERT: D 112 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.7164 (ttt-90) REVERT: E 53 GLN cc_start: 0.7753 (mm-40) cc_final: 0.7424 (tp-100) outliers start: 8 outliers final: 7 residues processed: 84 average time/residue: 2.0316 time to fit residues: 190.8405 Evaluate side-chains 81 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 589 ASP Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 36 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 113 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.213278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.133289 restraints weight = 55128.448| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.42 r_work: 0.3470 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12098 Z= 0.206 Angle : 0.550 10.088 16442 Z= 0.297 Chirality : 0.044 0.159 1787 Planarity : 0.004 0.072 2164 Dihedral : 4.132 20.090 1656 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.63 % Allowed : 10.10 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1495 helix: 2.08 (0.29), residues: 309 sheet: -0.02 (0.23), residues: 464 loop : -1.55 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 635 HIS 0.007 0.001 HIS A 533 PHE 0.017 0.002 PHE E 77 TYR 0.019 0.002 TYR D 62 ARG 0.007 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 532) hydrogen bonds : angle 4.73476 ( 1500) SS BOND : bond 0.00892 ( 1) SS BOND : angle 3.56896 ( 2) covalent geometry : bond 0.00494 (12097) covalent geometry : angle 0.54855 (16440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2990 Ramachandran restraints generated. 1495 Oldfield, 0 Emsley, 1495 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 TYR cc_start: 0.6333 (t80) cc_final: 0.6065 (t80) REVERT: B 123 TYR cc_start: 0.4774 (m-80) cc_final: 0.4539 (m-80) REVERT: B 226 MET cc_start: 0.5502 (tmm) cc_final: 0.4943 (pmm) REVERT: C 41 TYR cc_start: 0.7752 (p90) cc_final: 0.5358 (t80) REVERT: D 48 TRP cc_start: 0.5478 (m100) cc_final: 0.4040 (m-90) REVERT: E 53 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7410 (tp-100) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 2.0444 time to fit residues: 191.6969 Evaluate side-chains 79 residues out of total 1267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain E residue 31 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 118 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4692 r_free = 0.4692 target = 0.215054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.131780 restraints weight = 54965.761| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.72 r_work: 0.3524 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12098 Z= 0.111 Angle : 0.492 10.833 16442 Z= 0.262 Chirality : 0.042 0.132 1787 Planarity : 0.004 0.061 2164 Dihedral : 3.944 18.221 1656 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.55 % Allowed : 10.18 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1495 helix: 2.39 (0.29), residues: 310 sheet: 0.02 (0.23), residues: 467 loop : -1.43 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.003 0.001 HIS B 121 PHE 0.011 0.001 PHE A 804 TYR 0.016 0.001 TYR A 465 ARG 0.005 0.000 ARG A 160 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 532) hydrogen bonds : angle 4.53882 ( 1500) SS BOND : bond 0.00665 ( 1) SS BOND : angle 2.85595 ( 2) covalent geometry : bond 0.00242 (12097) covalent geometry : angle 0.49099 (16440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18040.13 seconds wall clock time: 308 minutes 20.40 seconds (18500.40 seconds total)