Starting phenix.real_space_refine on Sun Sep 13 10:37:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nbx_12262/09_2026/7nbx_12262.map" } resolution = 4.8 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= 0.004 sd= 0.037 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 7251 2.51 5 N 1968 2.21 5 O 2257 1.98 5 H 11129 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 11784 Classifications: {'peptide': 761} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 733} Chain breaks: 1 Chain: "B" Number of atoms: 5307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 5307 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 11, 'TRANS': 345} Chain breaks: 1 Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 817 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 6, 'TRANS': 49} Chain: "D" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3459 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1270 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Time building chain proxies: 4.29, per 1000 atoms: 0.19 Number of scatterers: 22637 At special positions: 0 Unit cell: (117.7, 141.24, 103.79, 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 2257 8.00 N 1968 7.00 C 7251 6.00 H 11129 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 665 " 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: 2.31 Conformation dependent library (CDL) restraints added in 636.1 milliseconds 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2692 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 18 sheets defined 22.0% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 38 through 46 removed outlier: 3.713A pdb=" N MET A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 215 through 231 removed outlier: 3.634A pdb=" N LEU A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.633A pdb=" N ILE A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 286 " --> pdb=" O ALA A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 380 through 393 removed outlier: 3.924A pdb=" N LEU A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 removed outlier: 4.414A pdb=" N TRP A 546 " --> pdb=" O GLN A 542 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 548 " --> pdb=" O ALA A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.914A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 62 removed outlier: 3.975A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 removed outlier: 3.674A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.538A pdb=" N GLU D 178 " --> pdb=" O LEU D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.875A pdb=" N GLY D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.773A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 225 removed outlier: 3.717A pdb=" N MET D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.669A pdb=" N ILE E 46 " --> pdb=" O VAL E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.641A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 6.064A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 8.018A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLY A 253 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU A 247 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 255 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL A 245 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR A 257 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR A 243 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN A 259 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA5, first strand: chain 'A' and resid 351 through 355 removed outlier: 6.776A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N VAL A 418 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU A 355 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU A 420 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ASP A 413 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N THR A 402 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 415 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR A 400 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LYS A 417 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL A 398 " --> pdb=" O LYS A 417 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 427 through 429 removed outlier: 3.943A pdb=" N GLY A 443 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL A 483 " --> pdb=" O TYR A 477 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 628 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 630 " --> pdb=" O GLU A 717 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 636 " --> pdb=" O MET A 711 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 672 removed outlier: 3.966A pdb=" N ALA A 672 " --> pdb=" O ASP A 703 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASP A 703 " --> pdb=" O ALA A 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.530A 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 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB2, first strand: chain 'B' and resid 117 through 118 removed outlier: 6.688A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.413A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 201 through 203 Processing sheet with id=AB5, first strand: chain 'B' and resid 252 through 253 removed outlier: 3.784A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.537A pdb=" N LEU B 298 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP B 317 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 331 through 332 removed outlier: 3.927A pdb=" N VAL B 331 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 338 " --> pdb=" O VAL B 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 348 removed outlier: 3.757A pdb=" N GLN B 360 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 33 through 35 456 hydrogen bonds defined for protein. 1272 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: 5.37 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 11129 1.03 - 1.22: 4 1.22 - 1.42: 5068 1.42 - 1.62: 6621 1.62 - 1.82: 62 Bond restraints: 22884 Sorted by residual: bond pdb=" N PHE A 517 " pdb=" CA PHE A 517 " ideal model delta sigma weight residual 1.456 1.430 0.026 1.04e-02 9.25e+03 6.10e+00 bond pdb=" CA ASN E 106 " pdb=" CB ASN E 106 " ideal model delta sigma weight residual 1.527 1.496 0.030 1.27e-02 6.20e+03 5.74e+00 bond pdb=" CA ASN A 709 " pdb=" CB ASN A 709 " ideal model delta sigma weight residual 1.536 1.505 0.031 1.46e-02 4.69e+03 4.62e+00 bond pdb=" C GLY D 65 " pdb=" N PRO D 66 " ideal model delta sigma weight residual 1.337 1.313 0.024 1.24e-02 6.50e+03 3.74e+00 bond pdb=" CB TRP B 143 " pdb=" CG TRP B 143 " ideal model delta sigma weight residual 1.498 1.440 0.058 3.10e-02 1.04e+03 3.45e+00 ... (remaining 22879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 39467 2.02 - 4.03: 1580 4.03 - 6.05: 108 6.05 - 8.07: 11 8.07 - 10.09: 3 Bond angle restraints: 41169 Sorted by residual: angle pdb=" N GLY B 211 " pdb=" CA GLY B 211 " pdb=" C GLY B 211 " ideal model delta sigma weight residual 111.85 104.09 7.76 1.06e+00 8.90e-01 5.37e+01 angle pdb=" C LEU B 152 " pdb=" N SER B 153 " pdb=" CA SER B 153 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" N VAL D 192 " pdb=" CA VAL D 192 " pdb=" CB VAL D 192 " ideal model delta sigma weight residual 111.64 107.99 3.65 8.20e-01 1.49e+00 1.98e+01 angle pdb=" N ASN A 448 " pdb=" CA ASN A 448 " pdb=" C ASN A 448 " ideal model delta sigma weight residual 110.44 105.23 5.21 1.20e+00 6.94e-01 1.89e+01 angle pdb=" N ASN E 41 " pdb=" CA ASN E 41 " pdb=" C ASN E 41 " ideal model delta sigma weight residual 114.56 109.19 5.37 1.27e+00 6.20e-01 1.79e+01 ... (remaining 41164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9307 17.75 - 35.49: 1116 35.49 - 53.24: 279 53.24 - 70.99: 112 70.99 - 88.73: 34 Dihedral angle restraints: 10848 sinusoidal: 5851 harmonic: 4997 Sorted by residual: dihedral pdb=" CA SER A 557 " pdb=" C SER A 557 " pdb=" N THR A 558 " pdb=" CA THR A 558 " ideal model delta harmonic sigma weight residual 180.00 130.70 49.30 0 5.00e+00 4.00e-02 9.72e+01 dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N SER B 153 " pdb=" CA SER B 153 " ideal model delta harmonic sigma weight residual 180.00 -135.51 -44.49 0 5.00e+00 4.00e-02 7.92e+01 dihedral pdb=" CA PRO B 371 " pdb=" C PRO B 371 " pdb=" N VAL B 372 " pdb=" CA VAL B 372 " ideal model delta harmonic sigma weight residual 180.00 146.12 33.88 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 10845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1219 0.048 - 0.095: 413 0.095 - 0.143: 103 0.143 - 0.191: 13 0.191 - 0.238: 2 Chirality restraints: 1750 Sorted by residual: chirality pdb=" CG LEU A 450 " pdb=" CB LEU A 450 " pdb=" CD1 LEU A 450 " pdb=" CD2 LEU A 450 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 505 " pdb=" CA THR A 505 " pdb=" OG1 THR A 505 " pdb=" CG2 THR A 505 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1747 not shown) Planarity restraints: 3509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 370 " 0.057 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO B 371 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 555 " -0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO A 556 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 556 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 556 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 374 " -0.012 2.00e-02 2.50e+03 2.54e-02 6.46e+00 pdb=" C ALA B 374 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 374 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 375 " -0.015 2.00e-02 2.50e+03 ... (remaining 3506 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 2542 2.22 - 2.82: 50800 2.82 - 3.41: 60149 3.41 - 4.01: 78690 4.01 - 4.60: 115940 Nonbonded interactions: 308121 Sorted by model distance: nonbonded pdb=" H SER A 269 " pdb=" O VAL A 335 " model vdw 1.626 2.450 nonbonded pdb=" O MET A 539 " pdb="HD21 ASN A 563 " model vdw 1.637 2.450 nonbonded pdb=" O THR A 190 " pdb=" H ILE A 194 " model vdw 1.658 2.450 nonbonded pdb=" OD2 ASP A 410 " pdb=" H THR E 61 " model vdw 1.658 2.450 nonbonded pdb=" O SER C 73 " pdb=" HG1 THR D 161 " model vdw 1.661 2.450 ... (remaining 308116 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.970 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: 0.140 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.260 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 : 0.008 0.062 11756 Z= 0.402 Angle : 1.043 10.086 15978 Z= 0.619 Chirality : 0.050 0.238 1750 Planarity : 0.006 0.085 2102 Dihedral : 15.897 88.734 4252 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.25 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -4.49 (0.18), residues: 1461 helix: -2.41 (0.22), residues: 283 sheet: -2.37 (0.22), residues: 378 loop : -3.62 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 173 TYR 0.020 0.003 TYR A 255 PHE 0.024 0.002 PHE A 565 TRP 0.022 0.003 TRP A 376 HIS 0.011 0.003 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.40 (11755) covalent geometry : angle 1.04290 / 0.62 (15976) SS BOND : bond 0.00045 / 0.02 ( 1) SS BOND : angle 1.50766 / 0.83 ( 2) hydrogen bonds : bond 0.15088 / 9.94 ( 456) hydrogen bonds : angle 8.56883 / 6.06 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.600 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: 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: 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 241 ASP cc_start: 0.9127 (m-30) cc_final: 0.8802 (m-30) REVERT: A 503 ASP cc_start: 0.8686 (t0) cc_final: 0.8366 (m-30) REVERT: A 523 ASN cc_start: 0.8839 (m110) cc_final: 0.8395 (m-40) REVERT: A 652 PHE cc_start: 0.8008 (m-80) cc_final: 0.7754 (m-10) REVERT: A 671 LYS cc_start: 0.8882 (pttm) cc_final: 0.8488 (ptpp) REVERT: B 165 HIS cc_start: 0.8274 (t-90) cc_final: 0.7677 (t-90) REVERT: B 367 PHE cc_start: 0.8990 (m-80) cc_final: 0.8713 (m-80) REVERT: D 34 GLU cc_start: 0.9492 (mp0) cc_final: 0.9188 (pm20) REVERT: D 109 MET cc_start: 0.9240 (mmm) cc_final: 0.8814 (mtp) REVERT: D 148 SER cc_start: 0.9579 (m) cc_final: 0.9369 (p) REVERT: D 183 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8840 (tt0) REVERT: D 219 GLU cc_start: 0.8814 (tp30) cc_final: 0.8599 (tp30) REVERT: E 36 ASN cc_start: 0.9346 (m-40) cc_final: 0.8706 (t0) REVERT: E 50 MET cc_start: 0.8702 (mtp) cc_final: 0.8082 (mtp) REVERT: E 107 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8963 (mmtp) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1925 time to fit residues: 44.6563 Evaluate side-chains 113 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 161 ASN A 170 GLN A 286 GLN A 323 GLN A 411 GLN A 441 GLN A 523 ASN A 540 GLN A 561 GLN A 801 GLN A 805 ASN B 40 ASN B 70 ASN B 85 ASN B 130 GLN B 144 GLN B 170 GLN B 319 GLN B 360 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 82 ASN E 36 ASN E 53 GLN E 54 GLN E 103 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.065020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.048154 restraints weight = 171881.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.051116 restraints weight = 78669.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.053103 restraints weight = 45110.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.054421 restraints weight = 29791.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055345 restraints weight = 22175.971| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11756 Z= 0.153 Angle : 0.674 6.125 15978 Z= 0.371 Chirality : 0.044 0.155 1750 Planarity : 0.005 0.071 2102 Dihedral : 7.491 44.601 1615 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.75 % Favored : 89.12 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.56 (0.19), residues: 1461 helix: -1.00 (0.26), residues: 300 sheet: -2.04 (0.22), residues: 383 loop : -3.19 (0.20), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 355 TYR 0.015 0.002 TYR D 177 PHE 0.016 0.001 PHE D 95 TRP 0.016 0.002 TRP A 546 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (11755) covalent geometry : angle 0.67391 / 0.37 (15976) SS BOND : bond 0.00034 / 0.02 ( 1) SS BOND : angle 1.20743 / 0.67 ( 2) hydrogen bonds : bond 0.04715 / 3.25 ( 456) hydrogen bonds : angle 7.05501 / 5.00 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.591 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: 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: 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 369 MET cc_start: 0.9245 (mmt) cc_final: 0.9035 (mmt) REVERT: A 387 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8778 (mt-10) REVERT: A 503 ASP cc_start: 0.8624 (t0) cc_final: 0.8411 (m-30) REVERT: B 165 HIS cc_start: 0.8272 (t-90) cc_final: 0.7657 (t-90) REVERT: B 369 THR cc_start: 0.9788 (p) cc_final: 0.9543 (t) REVERT: D 34 GLU cc_start: 0.9508 (mp0) cc_final: 0.9186 (pm20) REVERT: D 178 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8777 (mm-30) REVERT: D 201 MET cc_start: 0.9257 (mtp) cc_final: 0.8795 (mtp) REVERT: D 219 GLU cc_start: 0.8760 (tp30) cc_final: 0.8476 (tp30) REVERT: E 50 MET cc_start: 0.8771 (mtp) cc_final: 0.8247 (mtp) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1793 time to fit residues: 39.4640 Evaluate side-chains 115 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 138 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 24 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 136 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN A 403 GLN A 506 ASN B 324 HIS ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN D 60 ASN E 52 GLN E 83 HIS E 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.044927 restraints weight = 170378.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.047675 restraints weight = 79898.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.049552 restraints weight = 46728.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.050856 restraints weight = 31466.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.051692 restraints weight = 23377.262| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11756 Z= 0.292 Angle : 0.719 7.115 15978 Z= 0.400 Chirality : 0.043 0.175 1750 Planarity : 0.005 0.072 2102 Dihedral : 7.037 41.978 1615 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.59 % Favored : 87.27 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.56 (0.20), residues: 1461 helix: -0.83 (0.27), residues: 299 sheet: -2.19 (0.22), residues: 430 loop : -3.19 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 212 TYR 0.018 0.002 TYR A 504 PHE 0.020 0.002 PHE D 95 TRP 0.017 0.002 TRP A 376 HIS 0.009 0.002 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.29 (11755) covalent geometry : angle 0.71870 / 0.40 (15976) SS BOND : bond 0.00133 / 0.07 ( 1) SS BOND : angle 1.35928 / 0.76 ( 2) hydrogen bonds : bond 0.04394 / 3.00 ( 456) hydrogen bonds : angle 6.92218 / 4.94 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.434 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: 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: 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 369 MET cc_start: 0.9496 (mmt) cc_final: 0.9126 (mmt) REVERT: A 503 ASP cc_start: 0.8755 (t0) cc_final: 0.8380 (m-30) REVERT: A 671 LYS cc_start: 0.8721 (pttm) cc_final: 0.8223 (ptpp) REVERT: B 165 HIS cc_start: 0.8212 (t-90) cc_final: 0.7880 (t70) REVERT: C 81 ASP cc_start: 0.8547 (t0) cc_final: 0.8329 (t0) REVERT: D 34 GLU cc_start: 0.9480 (mp0) cc_final: 0.9158 (pm20) REVERT: D 178 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8960 (mm-30) REVERT: D 219 GLU cc_start: 0.8748 (tp30) cc_final: 0.8148 (tp30) REVERT: E 36 ASN cc_start: 0.9374 (m110) cc_final: 0.8588 (m-40) REVERT: E 50 MET cc_start: 0.9039 (mtp) cc_final: 0.8524 (mtp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1714 time to fit residues: 34.2023 Evaluate side-chains 110 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 83 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 18 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 71.2527 > 50:) chunk 1 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.047121 restraints weight = 169502.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.049968 restraints weight = 78034.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.051901 restraints weight = 45315.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.053122 restraints weight = 30399.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054050 restraints weight = 23011.327| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11756 Z= 0.144 Angle : 0.593 5.920 15978 Z= 0.325 Chirality : 0.043 0.151 1750 Planarity : 0.004 0.069 2102 Dihedral : 6.415 39.188 1615 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.86 % Favored : 90.01 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.03 (0.20), residues: 1461 helix: -0.15 (0.28), residues: 302 sheet: -1.86 (0.22), residues: 409 loop : -2.97 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 366 TYR 0.012 0.001 TYR A 504 PHE 0.015 0.001 PHE D 95 TRP 0.017 0.001 TRP A 376 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (11755) covalent geometry : angle 0.59326 / 0.32 (15976) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 1.10489 / 0.61 ( 2) hydrogen bonds : bond 0.03863 / 2.65 ( 456) hydrogen bonds : angle 6.34416 / 4.52 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.657 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: 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: 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 369 MET cc_start: 0.9552 (mmt) cc_final: 0.9220 (mmt) REVERT: A 503 ASP cc_start: 0.8686 (t0) cc_final: 0.8402 (m-30) REVERT: A 539 MET cc_start: 0.8604 (mpp) cc_final: 0.8394 (mpp) REVERT: A 652 PHE cc_start: 0.7901 (m-80) cc_final: 0.7480 (m-10) REVERT: B 165 HIS cc_start: 0.8334 (t-90) cc_final: 0.7984 (t70) REVERT: C 81 ASP cc_start: 0.8559 (t0) cc_final: 0.8331 (t0) REVERT: D 34 GLU cc_start: 0.9447 (mp0) cc_final: 0.9112 (pm20) REVERT: D 178 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8701 (mm-30) REVERT: D 208 THR cc_start: 0.8365 (m) cc_final: 0.8153 (p) REVERT: D 219 GLU cc_start: 0.8771 (tp30) cc_final: 0.8163 (tp30) REVERT: E 36 ASN cc_start: 0.9485 (m-40) cc_final: 0.9064 (m-40) REVERT: E 50 MET cc_start: 0.9050 (mtp) cc_final: 0.8421 (mtp) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1781 time to fit residues: 38.0628 Evaluate side-chains 115 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 128 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 2 optimal weight: 30.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.044952 restraints weight = 165419.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.047741 restraints weight = 76959.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049667 restraints weight = 44875.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.050973 restraints weight = 30107.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.051885 restraints weight = 22371.445| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 11756 Z= 0.222 Angle : 0.628 6.218 15978 Z= 0.347 Chirality : 0.042 0.148 1750 Planarity : 0.005 0.071 2102 Dihedral : 6.234 36.976 1615 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.25 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.12 (0.20), residues: 1461 helix: -0.32 (0.28), residues: 302 sheet: -1.84 (0.22), residues: 438 loop : -3.05 (0.21), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 243 TYR 0.013 0.002 TYR A 504 PHE 0.022 0.002 PHE D 95 TRP 0.019 0.002 TRP A 376 HIS 0.007 0.002 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.22 (11755) covalent geometry : angle 0.62764 / 0.35 (15976) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 1.25179 / 0.70 ( 2) hydrogen bonds : bond 0.03854 / 2.63 ( 456) hydrogen bonds : angle 6.33502 / 4.52 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.616 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: 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: 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 503 ASP cc_start: 0.8761 (t0) cc_final: 0.8415 (m-30) REVERT: A 615 THR cc_start: 0.8371 (m) cc_final: 0.8169 (m) REVERT: C 81 ASP cc_start: 0.8617 (t0) cc_final: 0.8344 (t0) REVERT: D 34 GLU cc_start: 0.9437 (mp0) cc_final: 0.9121 (pm20) REVERT: D 178 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8763 (mm-30) REVERT: E 36 ASN cc_start: 0.9454 (m-40) cc_final: 0.8753 (t0) REVERT: E 50 MET cc_start: 0.9036 (mtp) cc_final: 0.8565 (mtp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1839 time to fit residues: 36.9683 Evaluate side-chains 115 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 59 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 533 HIS ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.062891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.045489 restraints weight = 163046.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.048366 restraints weight = 74382.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.050328 restraints weight = 42922.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051656 restraints weight = 28607.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.052519 restraints weight = 21232.677| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11756 Z= 0.159 Angle : 0.575 5.891 15978 Z= 0.316 Chirality : 0.042 0.150 1750 Planarity : 0.004 0.068 2102 Dihedral : 5.931 35.168 1615 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.20 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.85 (0.21), residues: 1461 helix: 0.09 (0.29), residues: 304 sheet: -1.79 (0.23), residues: 425 loop : -2.89 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.014 0.001 TYR A 754 PHE 0.019 0.001 PHE D 95 TRP 0.017 0.001 TRP A 376 HIS 0.011 0.002 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (11755) covalent geometry : angle 0.57490 / 0.32 (15976) SS BOND : bond 0.00088 / 0.05 ( 1) SS BOND : angle 1.10705 / 0.62 ( 2) hydrogen bonds : bond 0.03602 / 2.46 ( 456) hydrogen bonds : angle 6.08416 / 4.35 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.621 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: 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: 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 503 ASP cc_start: 0.8752 (t0) cc_final: 0.8427 (m-30) REVERT: A 615 THR cc_start: 0.8390 (m) cc_final: 0.8182 (m) REVERT: C 81 ASP cc_start: 0.8603 (t0) cc_final: 0.8357 (t0) REVERT: D 34 GLU cc_start: 0.9383 (mp0) cc_final: 0.9093 (pm20) REVERT: D 74 ASP cc_start: 0.9185 (m-30) cc_final: 0.8981 (m-30) REVERT: D 178 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8715 (mm-30) REVERT: E 36 ASN cc_start: 0.9507 (m-40) cc_final: 0.8796 (t0) REVERT: E 50 MET cc_start: 0.9054 (mtp) cc_final: 0.8629 (mtp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1873 time to fit residues: 39.4521 Evaluate side-chains 118 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 1 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.044561 restraints weight = 173582.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.047270 restraints weight = 80611.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.049146 restraints weight = 47246.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.050362 restraints weight = 31922.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.051244 restraints weight = 24172.882| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11756 Z= 0.283 Angle : 0.660 6.682 15978 Z= 0.367 Chirality : 0.042 0.147 1750 Planarity : 0.005 0.071 2102 Dihedral : 6.065 36.051 1615 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.28 % Favored : 86.58 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.17 (0.20), residues: 1461 helix: -0.47 (0.27), residues: 304 sheet: -1.85 (0.23), residues: 441 loop : -3.05 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.021 0.002 TYR A 416 PHE 0.023 0.002 PHE D 95 TRP 0.017 0.002 TRP A 376 HIS 0.007 0.002 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.28 (11755) covalent geometry : angle 0.65947 / 0.37 (15976) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 1.20360 / 0.67 ( 2) hydrogen bonds : bond 0.03828 / 2.60 ( 456) hydrogen bonds : angle 6.34087 / 4.55 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.424 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: 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: 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 503 ASP cc_start: 0.8840 (t0) cc_final: 0.8385 (m-30) REVERT: A 615 THR cc_start: 0.8399 (m) cc_final: 0.8195 (m) REVERT: C 81 ASP cc_start: 0.8692 (t0) cc_final: 0.8447 (t0) REVERT: D 34 GLU cc_start: 0.9409 (mp0) cc_final: 0.9126 (pm20) REVERT: D 42 LYS cc_start: 0.9352 (mmtt) cc_final: 0.8909 (mmmm) REVERT: D 178 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8752 (mm-30) REVERT: E 36 ASN cc_start: 0.9478 (m-40) cc_final: 0.8900 (m-40) REVERT: E 50 MET cc_start: 0.9095 (mtp) cc_final: 0.8598 (mtp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1761 time to fit residues: 35.9737 Evaluate side-chains 111 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 116 optimal weight: 0.0970 chunk 20 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.063600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.046057 restraints weight = 157261.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.048979 restraints weight = 71244.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.051009 restraints weight = 41051.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.052411 restraints weight = 27237.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.053300 restraints weight = 20076.217| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11756 Z= 0.104 Angle : 0.550 5.731 15978 Z= 0.296 Chirality : 0.043 0.153 1750 Planarity : 0.004 0.063 2102 Dihedral : 5.606 33.784 1615 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.15 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.47 (0.21), residues: 1461 helix: 0.53 (0.30), residues: 301 sheet: -1.48 (0.24), residues: 405 loop : -2.73 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 325 TYR 0.013 0.001 TYR A 504 PHE 0.017 0.001 PHE A 648 TRP 0.017 0.001 TRP A 376 HIS 0.006 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (11755) covalent geometry : angle 0.54996 / 0.30 (15976) SS BOND : bond 0.00141 / 0.07 ( 1) SS BOND : angle 0.87391 / 0.49 ( 2) hydrogen bonds : bond 0.03420 / 2.34 ( 456) hydrogen bonds : angle 5.77396 / 4.12 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.630 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: 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: 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 503 ASP cc_start: 0.8727 (t0) cc_final: 0.8421 (m-30) REVERT: B 165 HIS cc_start: 0.8274 (t-90) cc_final: 0.7817 (t70) REVERT: B 232 ILE cc_start: 0.9670 (pt) cc_final: 0.9299 (mt) REVERT: C 81 ASP cc_start: 0.8607 (t0) cc_final: 0.8365 (t0) REVERT: D 34 GLU cc_start: 0.9366 (mp0) cc_final: 0.9050 (pm20) REVERT: D 42 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8800 (mmmm) REVERT: D 178 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8624 (mm-30) REVERT: E 36 ASN cc_start: 0.9460 (m-40) cc_final: 0.9098 (m-40) REVERT: E 50 MET cc_start: 0.9041 (mtp) cc_final: 0.8554 (mtp) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1770 time to fit residues: 38.6698 Evaluate side-chains 117 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 84 optimal weight: 0.0470 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 805 ASN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.064279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.046919 restraints weight = 164206.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049810 restraints weight = 74780.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.051831 restraints weight = 43216.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.053175 restraints weight = 28893.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.054010 restraints weight = 21587.303| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11756 Z= 0.101 Angle : 0.534 7.285 15978 Z= 0.287 Chirality : 0.043 0.154 1750 Planarity : 0.004 0.061 2102 Dihedral : 5.288 32.165 1615 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.23 (0.22), residues: 1461 helix: 0.80 (0.30), residues: 307 sheet: -1.39 (0.24), residues: 419 loop : -2.61 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 243 TYR 0.013 0.001 TYR A 504 PHE 0.020 0.001 PHE A 648 TRP 0.018 0.001 TRP B 48 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (11755) covalent geometry : angle 0.53404 / 0.29 (15976) SS BOND : bond 0.00122 / 0.06 ( 1) SS BOND : angle 0.88195 / 0.49 ( 2) hydrogen bonds : bond 0.03204 / 2.20 ( 456) hydrogen bonds : angle 5.55853 / 3.96 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.652 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: 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: 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 503 ASP cc_start: 0.8711 (t0) cc_final: 0.8499 (m-30) REVERT: A 615 THR cc_start: 0.8498 (m) cc_final: 0.8298 (m) REVERT: B 232 ILE cc_start: 0.9685 (pt) cc_final: 0.9300 (mt) REVERT: C 81 ASP cc_start: 0.8708 (t0) cc_final: 0.8490 (t0) REVERT: D 34 GLU cc_start: 0.9361 (mp0) cc_final: 0.9054 (pm20) REVERT: D 178 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8621 (mm-30) REVERT: E 36 ASN cc_start: 0.9446 (m-40) cc_final: 0.9111 (m-40) REVERT: E 45 LYS cc_start: 0.9647 (mttm) cc_final: 0.9443 (mmmt) REVERT: E 50 MET cc_start: 0.8987 (mtp) cc_final: 0.8439 (mtp) REVERT: E 93 LEU cc_start: 0.9380 (mm) cc_final: 0.9049 (mm) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1742 time to fit residues: 38.1468 Evaluate side-chains 120 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 7 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 138 optimal weight: 0.0770 chunk 141 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.064116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.046791 restraints weight = 164722.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.049700 restraints weight = 74703.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.051716 restraints weight = 43141.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052994 restraints weight = 28758.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053969 restraints weight = 21678.131| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11756 Z= 0.110 Angle : 0.527 7.149 15978 Z= 0.284 Chirality : 0.042 0.152 1750 Planarity : 0.004 0.063 2102 Dihedral : 5.166 32.114 1615 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.12 (0.22), residues: 1461 helix: 0.99 (0.30), residues: 301 sheet: -1.35 (0.24), residues: 428 loop : -2.54 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 243 TYR 0.012 0.001 TYR A 504 PHE 0.016 0.001 PHE A 652 TRP 0.018 0.001 TRP A 376 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11755) covalent geometry : angle 0.52718 / 0.28 (15976) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 0.90394 / 0.51 ( 2) hydrogen bonds : bond 0.03123 / 2.15 ( 456) hydrogen bonds : angle 5.49063 / 3.92 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2922 Ramachandran restraints generated. 1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.629 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 THR cc_start: 0.8494 (m) cc_final: 0.8283 (m) REVERT: B 232 ILE cc_start: 0.9699 (pt) cc_final: 0.9333 (mt) REVERT: C 81 ASP cc_start: 0.8684 (t0) cc_final: 0.8442 (t0) REVERT: D 34 GLU cc_start: 0.9349 (mp0) cc_final: 0.9048 (pm20) REVERT: D 178 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8745 (mm-30) REVERT: E 36 ASN cc_start: 0.9478 (m-40) cc_final: 0.9133 (m-40) REVERT: E 50 MET cc_start: 0.8950 (mtp) cc_final: 0.8473 (mtp) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1897 time to fit residues: 40.6585 Evaluate side-chains 113 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 63 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 82 optimal weight: 0.0020 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 775 GLN ** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.064157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.046435 restraints weight = 155365.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.049445 restraints weight = 70050.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.051517 restraints weight = 40242.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.052939 restraints weight = 26666.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.053819 restraints weight = 19658.735| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11756 Z= 0.097 Angle : 0.515 5.638 15978 Z= 0.275 Chirality : 0.042 0.152 1750 Planarity : 0.004 0.063 2102 Dihedral : 5.001 31.510 1615 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.94 (0.22), residues: 1461 helix: 1.14 (0.30), residues: 301 sheet: -1.29 (0.24), residues: 431 loop : -2.40 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.011 0.001 TYR A 504 PHE 0.012 0.001 PHE D 95 TRP 0.016 0.001 TRP A 376 HIS 0.004 0.001 HIS B 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (11755) covalent geometry : angle 0.51518 / 0.28 (15976) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 0.83787 / 0.47 ( 2) hydrogen bonds : bond 0.03028 / 2.09 ( 456) hydrogen bonds : angle 5.36523 / 3.83 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3103.33 seconds wall clock time: 54 minutes 10.21 seconds (3250.21 seconds total)