Starting phenix.real_space_refine on Sat Aug 23 06:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oma_70610/08_2025/9oma_70610.map" } resolution = 4.14 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= -0.022 sd= 0.230 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6575 2.51 5 N 1760 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10325 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2232 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 12, 'TRANS': 266} Chain breaks: 1 Chain: "B" Number of atoms: 5959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5959 Classifications: {'peptide': 723} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 701} Chain breaks: 3 Chain: "C" Number of atoms: 680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 680 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 1 Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 763 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 691 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10325 At special positions: 0 Unit cell: (90.3, 110.08, 191.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1920 8.00 N 1760 7.00 C 6575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 53 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 73 " 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: 0.82 Conformation dependent library (CDL) restraints added in 387.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2450 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 56.4% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.789A pdb=" N TYR A 51 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.541A pdb=" N ILE A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 242 through 264 removed outlier: 3.535A pdb=" N LEU A 246 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.837A pdb=" N ILE A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'B' and resid 21 through 31 removed outlier: 3.729A pdb=" N ARG B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 53 removed outlier: 4.071A pdb=" N PHE B 44 " --> pdb=" O TRP B 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER B 45 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS B 48 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 82 Processing helix chain 'B' and resid 85 through 105 removed outlier: 4.174A pdb=" N ASP B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Processing helix chain 'B' and resid 147 through 168 removed outlier: 3.645A pdb=" N ILE B 151 " --> pdb=" O ILE B 147 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASN B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ARG B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP B 157 " --> pdb=" O ASN B 153 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 160 " --> pdb=" O GLN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 188 removed outlier: 4.584A pdb=" N VAL B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 202 Processing helix chain 'B' and resid 202 through 218 Processing helix chain 'B' and resid 218 through 223 removed outlier: 4.050A pdb=" N GLN B 223 " --> pdb=" O PRO B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'B' and resid 256 through 270 Processing helix chain 'B' and resid 273 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 289 through 301 removed outlier: 4.206A pdb=" N LEU B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 333 removed outlier: 4.392A pdb=" N ASP B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA B 328 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU B 331 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 359 removed outlier: 3.635A pdb=" N TYR B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 378 Processing helix chain 'B' and resid 406 through 417 removed outlier: 3.510A pdb=" N ASN B 410 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'B' and resid 426 through 442 removed outlier: 3.587A pdb=" N GLU B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 removed outlier: 3.685A pdb=" N ARG B 452 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 484 removed outlier: 3.538A pdb=" N MET B 476 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 491 Processing helix chain 'B' and resid 491 through 514 removed outlier: 3.524A pdb=" N MET B 513 " --> pdb=" O ALA B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 526 Processing helix chain 'B' and resid 533 through 537 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 597 through 608 removed outlier: 4.017A pdb=" N GLN B 608 " --> pdb=" O PHE B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 626 through 639 Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 689 through 694 removed outlier: 3.803A pdb=" N GLN B 693 " --> pdb=" O GLY B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 726 removed outlier: 4.087A pdb=" N ARG B 700 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 715 " --> pdb=" O ARG B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 742 removed outlier: 3.934A pdb=" N GLU B 740 " --> pdb=" O THR B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 745 No H-bonds generated for 'chain 'B' and resid 743 through 745' Processing helix chain 'B' and resid 749 through 763 removed outlier: 4.370A pdb=" N GLU B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 3.602A pdb=" N GLU C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.775A pdb=" N LEU D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'E' and resid 17 through 21 Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 50 through 68 removed outlier: 3.671A pdb=" N LYS E 56 " --> pdb=" O HIS E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 removed outlier: 3.821A pdb=" N ASN E 92 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 147 removed outlier: 7.161A pdb=" N SER A 83 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP A 161 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 188 " --> pdb=" O ASP A 161 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 163 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N CYS A 165 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLY A 185 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 200 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 195 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 531 through 532 removed outlier: 6.223A pdb=" N LEU B 531 " --> pdb=" O TRP C 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 579 through 585 Processing sheet with id=AA5, first strand: chain 'B' and resid 614 through 615 Processing sheet with id=AA6, first strand: chain 'B' and resid 675 through 676 Processing sheet with id=AA7, first strand: chain 'B' and resid 728 through 730 Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 77 Processing sheet with id=AA9, first strand: chain 'D' and resid 73 through 75 removed outlier: 3.777A pdb=" N ARG D 8 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D 15 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LYS E 16 " --> pdb=" O PHE D 15 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3383 1.34 - 1.46: 2207 1.46 - 1.58: 4819 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10520 Sorted by residual: bond pdb=" N THR B 695 " pdb=" CA THR B 695 " ideal model delta sigma weight residual 1.455 1.498 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" N ILE B 766 " pdb=" CA ILE B 766 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N ILE B 147 " pdb=" CA ILE B 147 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N ILE B 197 " pdb=" CA ILE B 197 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.21e-02 6.83e+03 8.51e+00 bond pdb=" N VAL B 619 " pdb=" CA VAL B 619 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.14e+00 ... (remaining 10515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 13748 1.92 - 3.85: 397 3.85 - 5.77: 39 5.77 - 7.69: 1 7.69 - 9.61: 1 Bond angle restraints: 14186 Sorted by residual: angle pdb=" CA THR B 696 " pdb=" C THR B 696 " pdb=" O THR B 696 " ideal model delta sigma weight residual 121.60 116.81 4.79 1.21e+00 6.83e-01 1.57e+01 angle pdb=" CA GLU B 259 " pdb=" C GLU B 259 " pdb=" O GLU B 259 " ideal model delta sigma weight residual 120.55 116.51 4.04 1.06e+00 8.90e-01 1.45e+01 angle pdb=" CA THR B 696 " pdb=" CB THR B 696 " pdb=" OG1 THR B 696 " ideal model delta sigma weight residual 109.60 104.46 5.14 1.50e+00 4.44e-01 1.17e+01 angle pdb=" CA THR B 695 " pdb=" C THR B 695 " pdb=" O THR B 695 " ideal model delta sigma weight residual 121.45 117.90 3.55 1.07e+00 8.73e-01 1.10e+01 angle pdb=" CA VAL B 258 " pdb=" C VAL B 258 " pdb=" O VAL B 258 " ideal model delta sigma weight residual 121.17 117.69 3.48 1.06e+00 8.90e-01 1.08e+01 ... (remaining 14181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 5836 16.33 - 32.66: 447 32.66 - 48.99: 131 48.99 - 65.32: 39 65.32 - 81.65: 18 Dihedral angle restraints: 6471 sinusoidal: 2723 harmonic: 3748 Sorted by residual: dihedral pdb=" CA LEU B 107 " pdb=" C LEU B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CB CYS C 50 " pdb=" SG CYS C 50 " pdb=" SG CYS C 53 " pdb=" CB CYS C 53 " ideal model delta sinusoidal sigma weight residual 93.00 133.81 -40.81 1 1.00e+01 1.00e-02 2.33e+01 dihedral pdb=" CA PRO D 72 " pdb=" C PRO D 72 " pdb=" N ALA D 73 " pdb=" CA ALA D 73 " ideal model delta harmonic sigma weight residual 180.00 158.42 21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1151 0.040 - 0.081: 297 0.081 - 0.121: 102 0.121 - 0.161: 18 0.161 - 0.202: 7 Chirality restraints: 1575 Sorted by residual: chirality pdb=" CA ILE B 766 " pdb=" N ILE B 766 " pdb=" C ILE B 766 " pdb=" CB ILE B 766 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA LEU B 694 " pdb=" N LEU B 694 " pdb=" C LEU B 694 " pdb=" CB LEU B 694 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA VAL B 619 " pdb=" N VAL B 619 " pdb=" C VAL B 619 " pdb=" CB VAL B 619 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.72e-01 ... (remaining 1572 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 43 " 0.270 9.50e-02 1.11e+02 1.21e-01 8.96e+00 pdb=" NE ARG D 43 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 43 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 43 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 43 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 107 " 0.039 5.00e-02 4.00e+02 5.95e-02 5.66e+00 pdb=" N PRO B 108 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 65 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 66 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " 0.028 5.00e-02 4.00e+02 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2905 2.81 - 3.34: 10492 3.34 - 3.86: 16801 3.86 - 4.38: 20026 4.38 - 4.90: 32841 Nonbonded interactions: 83065 Sorted by model distance: nonbonded pdb=" N TYR D 45 " pdb=" O LEU D 77 " model vdw 2.293 3.120 nonbonded pdb=" O GLY E 32 " pdb=" O PRO E 33 " model vdw 2.334 3.040 nonbonded pdb=" O ARG D 68 " pdb=" O ALA D 71 " model vdw 2.344 3.040 nonbonded pdb=" O GLY A 228 " pdb=" OG SER A 232 " model vdw 2.358 3.040 nonbonded pdb=" O ILE E 26 " pdb=" O MET E 29 " model vdw 2.403 3.040 ... (remaining 83060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 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 : 0.005 0.053 10522 Z= 0.292 Angle : 0.733 9.614 14190 Z= 0.444 Chirality : 0.044 0.202 1575 Planarity : 0.006 0.121 1818 Dihedral : 14.120 81.655 4015 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.46 % Favored : 94.14 % Rotamer: Outliers : 2.01 % Allowed : 8.55 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.24), residues: 1246 helix: 0.26 (0.21), residues: 618 sheet: -0.21 (0.63), residues: 59 loop : -1.17 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 17 TYR 0.017 0.002 TYR A 160 PHE 0.034 0.002 PHE E 13 TRP 0.016 0.001 TRP B 97 HIS 0.010 0.002 HIS A 173 Details of bonding type rmsd covalent geometry : bond 0.00533 (10520) covalent geometry : angle 0.73310 (14186) SS BOND : bond 0.00046 ( 2) SS BOND : angle 0.46611 ( 4) hydrogen bonds : bond 0.16183 ( 510) hydrogen bonds : angle 7.09491 ( 1470) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 266 time to evaluate : 0.338 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: B 144 ASN cc_start: 0.6910 (OUTLIER) cc_final: 0.6587 (t0) REVERT: B 188 CYS cc_start: 0.7768 (m) cc_final: 0.7384 (m) REVERT: B 249 LEU cc_start: 0.6761 (mt) cc_final: 0.6552 (mt) REVERT: B 292 LYS cc_start: 0.7857 (mttt) cc_final: 0.7621 (mttp) REVERT: B 492 LYS cc_start: 0.9034 (tttm) cc_final: 0.8752 (tptt) REVERT: B 672 PHE cc_start: 0.7863 (t80) cc_final: 0.7013 (t80) REVERT: B 682 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7614 (tptt) REVERT: B 762 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8112 (pt0) REVERT: D 41 GLU cc_start: 0.3384 (OUTLIER) cc_final: 0.2112 (mt-10) REVERT: E 11 HIS cc_start: 0.7038 (t70) cc_final: 0.6516 (t-90) REVERT: E 59 MET cc_start: 0.7415 (ttp) cc_final: 0.7145 (ttm) outliers start: 23 outliers final: 4 residues processed: 282 average time/residue: 0.1195 time to fit residues: 44.7678 Evaluate side-chains 181 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN B 32 GLN B 103 GLN ** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 475 ASN B 514 HIS B 599 GLN C 82 HIS C 109 GLN D 10 HIS ** E 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.107318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.092642 restraints weight = 60842.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.094210 restraints weight = 37179.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.095347 restraints weight = 25389.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.095968 restraints weight = 18806.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.096526 restraints weight = 15361.832| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 10522 Z= 0.193 Angle : 0.687 8.563 14190 Z= 0.362 Chirality : 0.044 0.172 1575 Planarity : 0.006 0.069 1818 Dihedral : 4.743 23.857 1366 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.98 % Favored : 94.78 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.23), residues: 1246 helix: 0.64 (0.21), residues: 627 sheet: 0.64 (0.66), residues: 54 loop : -1.29 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 417 TYR 0.018 0.002 TYR B 233 PHE 0.020 0.002 PHE A 216 TRP 0.051 0.002 TRP B 759 HIS 0.010 0.001 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00420 (10520) covalent geometry : angle 0.68735 (14186) SS BOND : bond 0.00073 ( 2) SS BOND : angle 0.49655 ( 4) hydrogen bonds : bond 0.05774 ( 510) hydrogen bonds : angle 5.31453 ( 1470) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.293 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: A 173 HIS cc_start: 0.7045 (m90) cc_final: 0.6453 (m-70) REVERT: B 188 CYS cc_start: 0.8042 (m) cc_final: 0.7365 (p) REVERT: B 629 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8471 (mt-10) REVERT: B 640 PHE cc_start: 0.7700 (t80) cc_final: 0.7286 (t80) REVERT: B 660 PHE cc_start: 0.7247 (m-80) cc_final: 0.6464 (m-10) REVERT: B 672 PHE cc_start: 0.6718 (t80) cc_final: 0.6186 (t80) REVERT: B 694 LEU cc_start: 0.7918 (mt) cc_final: 0.7690 (tp) REVERT: B 753 ILE cc_start: 0.9379 (pt) cc_final: 0.8532 (pt) REVERT: C 35 TRP cc_start: 0.1946 (t60) cc_final: 0.1356 (t60) REVERT: C 58 MET cc_start: -0.3289 (mmt) cc_final: -0.3545 (mtt) REVERT: D 31 VAL cc_start: 0.8204 (p) cc_final: 0.7957 (m) REVERT: D 89 CYS cc_start: 0.6394 (p) cc_final: 0.5678 (p) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1177 time to fit residues: 35.2449 Evaluate side-chains 173 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 79 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 223 GLN B 288 ASN B 498 GLN B 514 HIS ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.109100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.091276 restraints weight = 59227.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.092462 restraints weight = 37450.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.093598 restraints weight = 26918.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.094541 restraints weight = 21252.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.095106 restraints weight = 17756.686| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10522 Z= 0.157 Angle : 0.659 8.291 14190 Z= 0.341 Chirality : 0.043 0.188 1575 Planarity : 0.005 0.078 1818 Dihedral : 4.727 31.016 1366 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.57 % Favored : 95.18 % Rotamer: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.24), residues: 1246 helix: 0.58 (0.21), residues: 632 sheet: 0.46 (0.60), residues: 64 loop : -1.29 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 252 TYR 0.020 0.002 TYR B 562 PHE 0.033 0.002 PHE A 33 TRP 0.022 0.001 TRP B 759 HIS 0.009 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00344 (10520) covalent geometry : angle 0.65870 (14186) SS BOND : bond 0.00040 ( 2) SS BOND : angle 0.41253 ( 4) hydrogen bonds : bond 0.05185 ( 510) hydrogen bonds : angle 5.05629 ( 1470) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 0.421 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: A 173 HIS cc_start: 0.6920 (m90) cc_final: 0.6628 (m-70) REVERT: B 188 CYS cc_start: 0.7942 (m) cc_final: 0.7329 (p) REVERT: B 252 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7450 (ttm-80) REVERT: B 296 MET cc_start: 0.7762 (ttp) cc_final: 0.7501 (ttp) REVERT: B 361 ASP cc_start: 0.8191 (t0) cc_final: 0.7568 (t0) REVERT: B 629 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8573 (mt-10) REVERT: B 640 PHE cc_start: 0.8106 (t80) cc_final: 0.7690 (t80) REVERT: B 660 PHE cc_start: 0.7300 (m-80) cc_final: 0.6324 (m-10) REVERT: B 670 GLN cc_start: 0.7023 (mp10) cc_final: 0.6476 (tp-100) REVERT: B 694 LEU cc_start: 0.8293 (mt) cc_final: 0.7913 (tp) REVERT: B 743 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7887 (ptpt) REVERT: C 35 TRP cc_start: 0.2956 (t60) cc_final: 0.1761 (t60) REVERT: D 31 VAL cc_start: 0.8175 (p) cc_final: 0.7886 (m) outliers start: 3 outliers final: 0 residues processed: 210 average time/residue: 0.1158 time to fit residues: 32.6168 Evaluate side-chains 167 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 5.9990 chunk 68 optimal weight: 0.0040 chunk 79 optimal weight: 0.9980 chunk 22 optimal weight: 0.0270 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 49 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 120 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN B 223 GLN ** B 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.109562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.091655 restraints weight = 59599.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.093143 restraints weight = 36725.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.094381 restraints weight = 26084.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.095079 restraints weight = 20186.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.095828 restraints weight = 16969.923| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10522 Z= 0.133 Angle : 0.624 8.130 14190 Z= 0.322 Chirality : 0.042 0.175 1575 Planarity : 0.005 0.104 1818 Dihedral : 4.636 34.432 1366 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 2.18 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.24), residues: 1246 helix: 0.61 (0.21), residues: 639 sheet: 0.57 (0.60), residues: 64 loop : -1.30 (0.27), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 452 TYR 0.021 0.002 TYR A 69 PHE 0.016 0.002 PHE B 273 TRP 0.020 0.001 TRP B 759 HIS 0.007 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00285 (10520) covalent geometry : angle 0.62448 (14186) SS BOND : bond 0.00103 ( 2) SS BOND : angle 0.60990 ( 4) hydrogen bonds : bond 0.04631 ( 510) hydrogen bonds : angle 4.96467 ( 1470) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.427 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: A 18 LEU cc_start: 0.7954 (mp) cc_final: 0.7726 (mp) REVERT: A 173 HIS cc_start: 0.6805 (m90) cc_final: 0.6453 (m-70) REVERT: A 204 ASN cc_start: 0.8317 (p0) cc_final: 0.7871 (m-40) REVERT: A 339 MET cc_start: 0.7748 (mmm) cc_final: 0.7504 (mmm) REVERT: B 188 CYS cc_start: 0.7772 (m) cc_final: 0.7264 (p) REVERT: B 252 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7720 (ttm110) REVERT: B 629 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8554 (mm-30) REVERT: B 631 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7950 (mtt-85) REVERT: B 660 PHE cc_start: 0.7272 (m-80) cc_final: 0.6344 (m-10) REVERT: B 674 LEU cc_start: 0.8830 (tt) cc_final: 0.8544 (mp) REVERT: B 694 LEU cc_start: 0.8247 (mt) cc_final: 0.7855 (tp) REVERT: B 743 LYS cc_start: 0.8248 (ptpp) cc_final: 0.7948 (ptpt) REVERT: C 35 TRP cc_start: 0.2889 (t60) cc_final: 0.1839 (t60) REVERT: D 31 VAL cc_start: 0.8245 (p) cc_final: 0.7920 (m) outliers start: 1 outliers final: 0 residues processed: 204 average time/residue: 0.1224 time to fit residues: 33.4784 Evaluate side-chains 166 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 GLN B 498 GLN ** B 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN C 109 GLN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.108369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.091817 restraints weight = 59153.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.092471 restraints weight = 39347.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.093127 restraints weight = 29259.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.093754 restraints weight = 21682.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.093677 restraints weight = 18564.970| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10522 Z= 0.149 Angle : 0.634 6.988 14190 Z= 0.329 Chirality : 0.044 0.340 1575 Planarity : 0.005 0.095 1818 Dihedral : 4.729 37.880 1366 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 0.26 % Allowed : 2.97 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.24), residues: 1246 helix: 0.44 (0.20), residues: 641 sheet: 0.68 (0.61), residues: 64 loop : -1.32 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 711 TYR 0.018 0.002 TYR E 63 PHE 0.027 0.002 PHE A 33 TRP 0.064 0.002 TRP B 759 HIS 0.005 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00330 (10520) covalent geometry : angle 0.63382 (14186) SS BOND : bond 0.00106 ( 2) SS BOND : angle 0.58501 ( 4) hydrogen bonds : bond 0.04841 ( 510) hydrogen bonds : angle 4.89593 ( 1470) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.448 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: A 173 HIS cc_start: 0.6728 (m90) cc_final: 0.6370 (m-70) REVERT: A 204 ASN cc_start: 0.8439 (p0) cc_final: 0.7993 (m-40) REVERT: B 188 CYS cc_start: 0.7852 (m) cc_final: 0.7315 (p) REVERT: B 252 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.7807 (ttm110) REVERT: B 296 MET cc_start: 0.8009 (ttp) cc_final: 0.7694 (ttp) REVERT: B 629 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8619 (mm-30) REVERT: B 640 PHE cc_start: 0.7965 (t80) cc_final: 0.7445 (t80) REVERT: B 660 PHE cc_start: 0.7471 (m-80) cc_final: 0.6510 (m-10) REVERT: B 743 LYS cc_start: 0.8426 (ptpp) cc_final: 0.8161 (ptpt) REVERT: C 35 TRP cc_start: 0.3150 (t60) cc_final: 0.2115 (t60) REVERT: C 40 MET cc_start: 0.6481 (tmm) cc_final: 0.6274 (tmm) outliers start: 3 outliers final: 2 residues processed: 192 average time/residue: 0.1055 time to fit residues: 27.7439 Evaluate side-chains 167 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN B 229 ASN B 294 HIS B 575 HIS B 756 GLN C 109 GLN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.102155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.087995 restraints weight = 62617.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.089348 restraints weight = 38609.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.090380 restraints weight = 27093.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.091102 restraints weight = 20423.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.091634 restraints weight = 16519.548| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10522 Z= 0.218 Angle : 0.725 9.689 14190 Z= 0.377 Chirality : 0.046 0.310 1575 Planarity : 0.005 0.073 1818 Dihedral : 5.112 39.330 1366 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.10 % Favored : 93.74 % Rotamer: Outliers : 0.09 % Allowed : 2.09 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1246 helix: 0.17 (0.20), residues: 643 sheet: 0.57 (0.64), residues: 64 loop : -1.56 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 495 TYR 0.028 0.002 TYR E 63 PHE 0.027 0.002 PHE E 13 TRP 0.011 0.002 TRP B 635 HIS 0.008 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00497 (10520) covalent geometry : angle 0.72534 (14186) SS BOND : bond 0.00115 ( 2) SS BOND : angle 0.57890 ( 4) hydrogen bonds : bond 0.05902 ( 510) hydrogen bonds : angle 5.15581 ( 1470) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.451 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: A 173 HIS cc_start: 0.7161 (m-70) cc_final: 0.6597 (m-70) REVERT: A 204 ASN cc_start: 0.8516 (p0) cc_final: 0.8165 (m-40) REVERT: B 188 CYS cc_start: 0.7797 (m) cc_final: 0.7256 (p) REVERT: B 640 PHE cc_start: 0.7922 (t80) cc_final: 0.7371 (t80) REVERT: B 660 PHE cc_start: 0.7309 (m-80) cc_final: 0.6584 (m-10) REVERT: B 672 PHE cc_start: 0.7390 (t80) cc_final: 0.6966 (t80) REVERT: B 699 MET cc_start: 0.7225 (ttt) cc_final: 0.6995 (ttt) REVERT: B 743 LYS cc_start: 0.8422 (ptpp) cc_final: 0.8195 (ptpt) REVERT: B 775 THR cc_start: 0.8838 (m) cc_final: 0.8117 (p) REVERT: D 6 MET cc_start: 0.6889 (ppp) cc_final: 0.6011 (ttt) REVERT: E 6 ILE cc_start: 0.8084 (mp) cc_final: 0.7840 (mt) outliers start: 1 outliers final: 0 residues processed: 190 average time/residue: 0.1165 time to fit residues: 30.1566 Evaluate side-chains 159 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 223 GLN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.101872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.087660 restraints weight = 60309.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.089025 restraints weight = 37279.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.090089 restraints weight = 26037.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.090790 restraints weight = 19649.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.091063 restraints weight = 15837.581| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10522 Z= 0.206 Angle : 0.725 8.388 14190 Z= 0.381 Chirality : 0.047 0.321 1575 Planarity : 0.006 0.074 1818 Dihedral : 5.312 38.978 1366 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 0.09 % Allowed : 1.92 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.23), residues: 1246 helix: 0.10 (0.20), residues: 640 sheet: 0.59 (0.63), residues: 62 loop : -1.80 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 714 TYR 0.030 0.002 TYR B 765 PHE 0.029 0.002 PHE B 598 TRP 0.038 0.002 TRP B 759 HIS 0.022 0.002 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00466 (10520) covalent geometry : angle 0.72486 (14186) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.90076 ( 4) hydrogen bonds : bond 0.05959 ( 510) hydrogen bonds : angle 5.18481 ( 1470) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.310 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: A 173 HIS cc_start: 0.7125 (m-70) cc_final: 0.6522 (m-70) REVERT: A 204 ASN cc_start: 0.8513 (p0) cc_final: 0.8228 (m-40) REVERT: A 339 MET cc_start: 0.7974 (mmm) cc_final: 0.7590 (mmm) REVERT: B 591 TYR cc_start: 0.5721 (p90) cc_final: 0.5416 (p90) REVERT: B 640 PHE cc_start: 0.7969 (t80) cc_final: 0.7615 (t80) REVERT: B 660 PHE cc_start: 0.7549 (m-80) cc_final: 0.6803 (m-10) REVERT: B 672 PHE cc_start: 0.7482 (t80) cc_final: 0.7260 (t80) REVERT: B 775 THR cc_start: 0.8963 (m) cc_final: 0.8214 (p) REVERT: B 779 MET cc_start: 0.4073 (mpp) cc_final: 0.3761 (mmt) REVERT: C 40 MET cc_start: 0.7382 (tmm) cc_final: 0.7151 (tmm) REVERT: C 89 MET cc_start: 0.7164 (pmm) cc_final: 0.6732 (pmm) REVERT: D 6 MET cc_start: 0.7146 (ppp) cc_final: 0.6445 (ttt) REVERT: E 6 ILE cc_start: 0.8077 (mp) cc_final: 0.7834 (mt) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.1074 time to fit residues: 26.6628 Evaluate side-chains 154 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.1980 chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.102154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.088702 restraints weight = 62003.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.090093 restraints weight = 37507.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.091087 restraints weight = 25521.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.091627 restraints weight = 18798.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.092126 restraints weight = 15375.285| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10522 Z= 0.155 Angle : 0.687 9.688 14190 Z= 0.359 Chirality : 0.046 0.324 1575 Planarity : 0.005 0.073 1818 Dihedral : 5.086 39.192 1366 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.23), residues: 1246 helix: 0.08 (0.20), residues: 647 sheet: 0.67 (0.64), residues: 62 loop : -1.74 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 711 TYR 0.019 0.002 TYR B 765 PHE 0.020 0.002 PHE B 273 TRP 0.032 0.002 TRP C 35 HIS 0.025 0.002 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00338 (10520) covalent geometry : angle 0.68703 (14186) SS BOND : bond 0.00084 ( 2) SS BOND : angle 0.82131 ( 4) hydrogen bonds : bond 0.05325 ( 510) hydrogen bonds : angle 5.06720 ( 1470) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 HIS cc_start: 0.7079 (m-70) cc_final: 0.6466 (m-70) REVERT: A 204 ASN cc_start: 0.8506 (p0) cc_final: 0.8214 (m-40) REVERT: A 339 MET cc_start: 0.7773 (mmm) cc_final: 0.7515 (mmm) REVERT: B 640 PHE cc_start: 0.7880 (t80) cc_final: 0.7547 (t80) REVERT: B 660 PHE cc_start: 0.7665 (m-80) cc_final: 0.6889 (m-10) REVERT: B 672 PHE cc_start: 0.7238 (t80) cc_final: 0.6958 (t80) REVERT: B 759 TRP cc_start: 0.7662 (p-90) cc_final: 0.7452 (p-90) REVERT: B 775 THR cc_start: 0.8835 (m) cc_final: 0.8117 (p) REVERT: B 779 MET cc_start: 0.3839 (mpp) cc_final: 0.3482 (mmt) REVERT: C 40 MET cc_start: 0.7302 (tmm) cc_final: 0.7050 (tmm) REVERT: C 89 MET cc_start: 0.6955 (pmm) cc_final: 0.6518 (pmm) REVERT: D 6 MET cc_start: 0.6938 (ppp) cc_final: 0.6012 (ttt) REVERT: E 6 ILE cc_start: 0.8024 (mp) cc_final: 0.7795 (mt) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.1190 time to fit residues: 29.3279 Evaluate side-chains 156 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 119 optimal weight: 0.4980 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 GLN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.102796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.089246 restraints weight = 61930.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.090600 restraints weight = 37596.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.091608 restraints weight = 25890.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.092215 restraints weight = 19105.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.092761 restraints weight = 15505.285| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10522 Z= 0.143 Angle : 0.678 9.596 14190 Z= 0.350 Chirality : 0.045 0.257 1575 Planarity : 0.005 0.071 1818 Dihedral : 4.940 39.330 1366 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer: Outliers : 0.09 % Allowed : 0.96 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.23), residues: 1246 helix: 0.23 (0.20), residues: 649 sheet: 0.89 (0.65), residues: 62 loop : -1.70 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 495 TYR 0.016 0.002 TYR D 45 PHE 0.017 0.002 PHE B 273 TRP 0.068 0.002 TRP C 35 HIS 0.018 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00309 (10520) covalent geometry : angle 0.67774 (14186) SS BOND : bond 0.00082 ( 2) SS BOND : angle 0.72622 ( 4) hydrogen bonds : bond 0.04879 ( 510) hydrogen bonds : angle 4.98085 ( 1470) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.399 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: A 173 HIS cc_start: 0.7079 (m-70) cc_final: 0.6467 (m-70) REVERT: A 204 ASN cc_start: 0.8470 (p0) cc_final: 0.8228 (m-40) REVERT: A 339 MET cc_start: 0.7661 (mmm) cc_final: 0.7398 (mmm) REVERT: B 630 LEU cc_start: 0.8648 (mt) cc_final: 0.8429 (mt) REVERT: B 640 PHE cc_start: 0.7944 (t80) cc_final: 0.7594 (t80) REVERT: B 660 PHE cc_start: 0.7767 (m-80) cc_final: 0.6926 (m-10) REVERT: B 757 ILE cc_start: 0.9064 (pt) cc_final: 0.8655 (pt) REVERT: B 760 LEU cc_start: 0.9023 (mt) cc_final: 0.8685 (mt) REVERT: B 772 ASP cc_start: 0.7945 (t70) cc_final: 0.7712 (t70) REVERT: B 775 THR cc_start: 0.8928 (m) cc_final: 0.8201 (p) REVERT: B 779 MET cc_start: 0.3939 (mpp) cc_final: 0.3527 (mmt) REVERT: C 35 TRP cc_start: 0.5411 (t60) cc_final: 0.4655 (t60) REVERT: C 89 MET cc_start: 0.6938 (pmm) cc_final: 0.6471 (pmm) REVERT: E 6 ILE cc_start: 0.8021 (mp) cc_final: 0.7786 (mt) REVERT: E 59 MET cc_start: 0.6841 (tmm) cc_final: 0.6474 (mmm) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1228 time to fit residues: 29.5567 Evaluate side-chains 159 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 113 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 57 optimal weight: 0.0970 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 223 GLN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.103583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.089430 restraints weight = 60175.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.090888 restraints weight = 36247.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.091966 restraints weight = 24792.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.092525 restraints weight = 18282.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.092686 restraints weight = 15018.876| |-----------------------------------------------------------------------------| r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10522 Z= 0.140 Angle : 0.692 10.231 14190 Z= 0.359 Chirality : 0.045 0.299 1575 Planarity : 0.005 0.072 1818 Dihedral : 4.876 39.121 1366 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.70 % Favored : 94.14 % Rotamer: Outliers : 0.09 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.23), residues: 1246 helix: 0.32 (0.21), residues: 649 sheet: 0.94 (0.65), residues: 62 loop : -1.64 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 252 TYR 0.020 0.002 TYR D 45 PHE 0.016 0.001 PHE B 273 TRP 0.048 0.002 TRP C 35 HIS 0.022 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00300 (10520) covalent geometry : angle 0.69204 (14186) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.66016 ( 4) hydrogen bonds : bond 0.04765 ( 510) hydrogen bonds : angle 5.02427 ( 1470) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.408 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: A 173 HIS cc_start: 0.7185 (m-70) cc_final: 0.6630 (m-70) REVERT: A 196 THR cc_start: 0.6758 (p) cc_final: 0.5418 (p) REVERT: A 204 ASN cc_start: 0.8545 (p0) cc_final: 0.8283 (m-40) REVERT: B 231 MET cc_start: 0.6890 (mtp) cc_final: 0.6416 (mtp) REVERT: B 252 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7624 (ttm-80) REVERT: B 436 GLU cc_start: 0.7306 (tp30) cc_final: 0.7085 (mm-30) REVERT: B 591 TYR cc_start: 0.5722 (p90) cc_final: 0.5408 (p90) REVERT: B 630 LEU cc_start: 0.8631 (mt) cc_final: 0.8394 (mt) REVERT: B 640 PHE cc_start: 0.7940 (t80) cc_final: 0.7571 (t80) REVERT: B 660 PHE cc_start: 0.7814 (m-80) cc_final: 0.7094 (m-10) REVERT: B 759 TRP cc_start: 0.7583 (p-90) cc_final: 0.7245 (p-90) REVERT: B 772 ASP cc_start: 0.8006 (t70) cc_final: 0.7788 (t70) REVERT: B 775 THR cc_start: 0.8954 (m) cc_final: 0.8233 (p) REVERT: B 779 MET cc_start: 0.4162 (mpp) cc_final: 0.3888 (mmt) REVERT: C 89 MET cc_start: 0.7046 (pmm) cc_final: 0.6531 (pmm) REVERT: D 6 MET cc_start: 0.6760 (ppp) cc_final: 0.6322 (ttt) REVERT: E 59 MET cc_start: 0.6800 (tmm) cc_final: 0.6429 (mmm) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1234 time to fit residues: 29.1511 Evaluate side-chains 157 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 2 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.0870 chunk 21 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN B 223 GLN ** B 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 ASN D 49 GLN ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.102003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.088601 restraints weight = 61790.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.089976 restraints weight = 37197.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.090945 restraints weight = 25383.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091639 restraints weight = 18846.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.092004 restraints weight = 15001.011| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10522 Z= 0.151 Angle : 0.695 9.897 14190 Z= 0.362 Chirality : 0.045 0.228 1575 Planarity : 0.005 0.072 1818 Dihedral : 4.924 39.097 1366 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.78 % Favored : 94.06 % Rotamer: Outliers : 0.17 % Allowed : 0.61 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.23), residues: 1246 helix: 0.33 (0.20), residues: 649 sheet: 0.95 (0.66), residues: 62 loop : -1.66 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 252 TYR 0.022 0.002 TYR D 45 PHE 0.018 0.002 PHE B 273 TRP 0.039 0.002 TRP C 35 HIS 0.022 0.001 HIS B 763 Details of bonding type rmsd covalent geometry : bond 0.00332 (10520) covalent geometry : angle 0.69547 (14186) SS BOND : bond 0.00068 ( 2) SS BOND : angle 0.66654 ( 4) hydrogen bonds : bond 0.05012 ( 510) hydrogen bonds : angle 5.04930 ( 1470) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.37 seconds wall clock time: 36 minutes 27.94 seconds (2187.94 seconds total)