Starting phenix.real_space_refine on Wed Feb 4 13:21:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.map" model { file = "/net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lhv_63106/02_2026/9lhv_63106.cif" } resolution = 2.79 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= -0.000 sd= 0.053 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 62 5.16 5 C 7112 2.51 5 N 1662 2.21 5 O 1828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5269 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 644} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 5269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5269 Classifications: {'peptide': 666} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 643} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 63 Unusual residues: {'CLR': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.84, per 1000 atoms: 0.27 Number of scatterers: 10664 At special positions: 0 Unit cell: (100.3, 131.75, 95.2, 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 62 16.00 O 1828 8.00 N 1662 7.00 C 7112 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 549.0 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2488 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 81.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 41 through 62 removed outlier: 3.658A pdb=" N ALA A 45 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 4.176A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 removed outlier: 3.520A pdb=" N ALA A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.927A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 4.265A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.755A pdb=" N LYS A 133 " --> pdb=" O SER A 129 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 158 removed outlier: 3.657A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 180 removed outlier: 4.093A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Proline residue: A 174 - end of helix removed outlier: 3.568A pdb=" N LEU A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.551A pdb=" N GLY A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.598A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.576A pdb=" N PHE A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 4.602A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.652A pdb=" N SER A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.531A pdb=" N LEU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.650A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.273A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.542A pdb=" N PHE A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 405 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.859A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.763A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 517 through 539 Processing helix chain 'A' and resid 637 through 653 removed outlier: 3.937A pdb=" N GLN A 653 " --> pdb=" O GLN A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 5.498A pdb=" N ILE A 666 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 667 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 removed outlier: 5.802A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 757 removed outlier: 3.561A pdb=" N TYR A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'B' and resid 42 through 62 removed outlier: 3.587A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 80 removed outlier: 4.248A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 removed outlier: 3.904A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 98 removed outlier: 3.977A pdb=" N VAL B 98 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 4.277A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.540A pdb=" N LYS B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.590A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 Processing helix chain 'B' and resid 168 through 194 Proline residue: B 174 - end of helix removed outlier: 3.704A pdb=" N LEU B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.605A pdb=" N VAL B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 234 removed outlier: 3.582A pdb=" N PHE B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 250 removed outlier: 4.554A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 removed outlier: 3.794A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.527A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 318 Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.255A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 4.453A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 405 Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.759A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 removed outlier: 3.746A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 503 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 517 through 539 Processing helix chain 'B' and resid 639 through 653 removed outlier: 3.930A pdb=" N GLN B 653 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 3.722A pdb=" N HIS B 658 " --> pdb=" O GLN B 654 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 711 removed outlier: 5.839A pdb=" N GLY B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 757 removed outlier: 3.672A pdb=" N TYR B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 Processing helix chain 'B' and resid 798 through 812 Processing sheet with id=AA1, first strand: chain 'A' and resid 815 through 817 Processing sheet with id=AA2, first strand: chain 'B' and resid 781 through 782 755 hydrogen bonds defined for protein. 2247 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: 1.67 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1619 1.32 - 1.44: 2959 1.44 - 1.57: 6246 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 10918 Sorted by residual: bond pdb=" C ASN B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.30e-02 5.92e+03 2.67e+00 bond pdb=" CBC Y01 B1001 " pdb=" OAW Y01 B1001 " ideal model delta sigma weight residual 1.437 1.459 -0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" CAL Y01 A1001 " pdb=" CAX Y01 A1001 " ideal model delta sigma weight residual 1.540 1.518 0.022 2.00e-02 2.50e+03 1.18e+00 bond pdb=" CG1 ILE A 666 " pdb=" CD1 ILE A 666 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.16e+00 bond pdb=" C3 CLR A1002 " pdb=" O1 CLR A1002 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.13e+00 ... (remaining 10913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 14676 2.08 - 4.16: 127 4.16 - 6.23: 25 6.23 - 8.31: 10 8.31 - 10.39: 2 Bond angle restraints: 14840 Sorted by residual: angle pdb=" N PRO B 35 " pdb=" CA PRO B 35 " pdb=" CB PRO B 35 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N PRO A 35 " pdb=" CA PRO A 35 " pdb=" CB PRO A 35 " ideal model delta sigma weight residual 103.00 110.38 -7.38 1.10e+00 8.26e-01 4.50e+01 angle pdb=" CB MET B 429 " pdb=" CG MET B 429 " pdb=" SD MET B 429 " ideal model delta sigma weight residual 112.70 123.09 -10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" CA MET B 429 " pdb=" CB MET B 429 " pdb=" CG MET B 429 " ideal model delta sigma weight residual 114.10 107.42 6.68 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CB MET A 429 " pdb=" CG MET A 429 " pdb=" SD MET A 429 " ideal model delta sigma weight residual 112.70 122.70 -10.00 3.00e+00 1.11e-01 1.11e+01 ... (remaining 14835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 5903 16.41 - 32.82: 542 32.82 - 49.24: 110 49.24 - 65.65: 18 65.65 - 82.06: 3 Dihedral angle restraints: 6576 sinusoidal: 2712 harmonic: 3864 Sorted by residual: dihedral pdb=" CA CYS A 662 " pdb=" C CYS A 662 " pdb=" N LEU A 663 " pdb=" CA LEU A 663 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CG ARG A 130 " pdb=" CD ARG A 130 " pdb=" NE ARG A 130 " pdb=" CZ ARG A 130 " ideal model delta sinusoidal sigma weight residual 180.00 -135.37 -44.63 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CA LEU B 157 " pdb=" C LEU B 157 " pdb=" N TYR B 158 " pdb=" CA TYR B 158 " ideal model delta harmonic sigma weight residual -180.00 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 6573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1346 0.047 - 0.093: 358 0.093 - 0.140: 49 0.140 - 0.186: 3 0.186 - 0.233: 4 Chirality restraints: 1760 Sorted by residual: chirality pdb=" CA PRO B 35 " pdb=" N PRO B 35 " pdb=" C PRO B 35 " pdb=" CB PRO B 35 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA PRO A 35 " pdb=" N PRO A 35 " pdb=" C PRO A 35 " pdb=" CB PRO A 35 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU A 391 " pdb=" CB LEU A 391 " pdb=" CD1 LEU A 391 " pdb=" CD2 LEU A 391 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 ... (remaining 1757 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 662 " -0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C CYS A 662 " 0.030 2.00e-02 2.50e+03 pdb=" O CYS A 662 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 663 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 384 " 0.009 2.00e-02 2.50e+03 1.08e-02 2.03e+00 pdb=" CG PHE B 384 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 384 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 384 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 384 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 384 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 384 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 410 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO B 411 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " 0.017 5.00e-02 4.00e+02 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2145 2.78 - 3.31: 10506 3.31 - 3.84: 17774 3.84 - 4.37: 20139 4.37 - 4.90: 35344 Nonbonded interactions: 85908 Sorted by model distance: nonbonded pdb=" O SER A 251 " pdb=" OG SER A 255 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU B 746 " pdb=" NH1 ARG B 808 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR A 68 " pdb=" OE2 GLU A 801 " model vdw 2.294 3.040 nonbonded pdb=" O GLU A 823 " pdb=" OH TYR A 831 " model vdw 2.318 3.040 nonbonded pdb=" O VAL B 322 " pdb=" OG SER B 354 " model vdw 2.319 3.040 ... (remaining 85903 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.470 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10918 Z= 0.119 Angle : 0.537 10.388 14840 Z= 0.276 Chirality : 0.040 0.233 1760 Planarity : 0.004 0.033 1792 Dihedral : 12.843 82.059 4088 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.24), residues: 1316 helix: 2.29 (0.17), residues: 1002 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.016 0.001 TYR A 451 PHE 0.025 0.001 PHE B 384 TRP 0.006 0.001 TRP A 363 HIS 0.002 0.000 HIS B 758 Details of bonding type rmsd covalent geometry : bond 0.00244 (10918) covalent geometry : angle 0.53656 (14840) hydrogen bonds : bond 0.10683 ( 755) hydrogen bonds : angle 4.92645 ( 2247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.348 Fit side-chains REVERT: B 319 LEU cc_start: 0.6786 (tt) cc_final: 0.6249 (mt) REVERT: B 413 MET cc_start: 0.5791 (ptp) cc_final: 0.5532 (ptm) outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.4474 time to fit residues: 61.4402 Evaluate side-chains 98 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0470 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 overall best weight: 0.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.229147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.158809 restraints weight = 10545.882| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.56 r_work: 0.3334 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10918 Z= 0.162 Angle : 0.553 8.902 14840 Z= 0.285 Chirality : 0.042 0.150 1760 Planarity : 0.004 0.037 1792 Dihedral : 5.621 46.408 1688 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.55 % Allowed : 8.18 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.23), residues: 1316 helix: 2.25 (0.16), residues: 1004 sheet: None (None), residues: 0 loop : -1.29 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 808 TYR 0.017 0.001 TYR A 451 PHE 0.028 0.002 PHE B 221 TRP 0.006 0.001 TRP B 396 HIS 0.004 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00395 (10918) covalent geometry : angle 0.55254 (14840) hydrogen bonds : bond 0.05163 ( 755) hydrogen bonds : angle 3.97936 ( 2247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.402 Fit side-chains REVERT: A 204 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6594 (mp) REVERT: A 413 MET cc_start: 0.6747 (ptp) cc_final: 0.6267 (ptm) REVERT: A 654 GLN cc_start: 0.5685 (mt0) cc_final: 0.5460 (mm-40) REVERT: B 204 ILE cc_start: 0.7253 (mp) cc_final: 0.7012 (OUTLIER) REVERT: B 301 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6982 (mp) REVERT: B 413 MET cc_start: 0.6552 (ptp) cc_final: 0.6049 (ptm) REVERT: B 696 CYS cc_start: 0.7542 (m) cc_final: 0.7292 (m) outliers start: 18 outliers final: 10 residues processed: 115 average time/residue: 0.4135 time to fit residues: 53.2674 Evaluate side-chains 112 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 801 GLU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 495 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 70 optimal weight: 0.0980 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.0770 chunk 57 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B 97 ASN B 380 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.231719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155345 restraints weight = 10633.754| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.58 r_work: 0.3382 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10918 Z= 0.110 Angle : 0.471 7.728 14840 Z= 0.245 Chirality : 0.039 0.139 1760 Planarity : 0.004 0.033 1792 Dihedral : 5.364 49.536 1688 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 9.72 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.24), residues: 1316 helix: 2.44 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.20 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.016 0.001 TYR A 451 PHE 0.025 0.001 PHE A 221 TRP 0.004 0.001 TRP A 679 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00234 (10918) covalent geometry : angle 0.47057 (14840) hydrogen bonds : bond 0.04260 ( 755) hydrogen bonds : angle 3.78232 ( 2247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.405 Fit side-chains REVERT: A 90 MET cc_start: 0.8424 (tpt) cc_final: 0.8204 (tpp) REVERT: A 212 LEU cc_start: 0.8439 (tp) cc_final: 0.7992 (mm) REVERT: A 413 MET cc_start: 0.6669 (ptp) cc_final: 0.6195 (ptm) REVERT: B 301 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6952 (mp) REVERT: B 413 MET cc_start: 0.6592 (ptp) cc_final: 0.6155 (ptm) REVERT: B 801 GLU cc_start: 0.5472 (mp0) cc_final: 0.5252 (mp0) outliers start: 23 outliers final: 7 residues processed: 117 average time/residue: 0.3650 time to fit residues: 48.3015 Evaluate side-chains 109 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 661 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 85 optimal weight: 0.5980 chunk 79 optimal weight: 0.0770 chunk 67 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.231311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155596 restraints weight = 10761.733| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.57 r_work: 0.3437 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10918 Z= 0.117 Angle : 0.475 7.711 14840 Z= 0.247 Chirality : 0.039 0.142 1760 Planarity : 0.004 0.032 1792 Dihedral : 5.306 49.843 1688 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.72 % Allowed : 11.19 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.24), residues: 1316 helix: 2.46 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.19 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.016 0.001 TYR A 451 PHE 0.025 0.001 PHE A 221 TRP 0.004 0.001 TRP B 396 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00259 (10918) covalent geometry : angle 0.47473 (14840) hydrogen bonds : bond 0.04320 ( 755) hydrogen bonds : angle 3.74413 ( 2247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 97 ASN cc_start: 0.8387 (m110) cc_final: 0.8186 (m-40) REVERT: A 413 MET cc_start: 0.6644 (ptp) cc_final: 0.6193 (ptm) REVERT: B 204 ILE cc_start: 0.7149 (mp) cc_final: 0.6870 (OUTLIER) REVERT: B 413 MET cc_start: 0.6605 (ptp) cc_final: 0.6155 (ptm) outliers start: 20 outliers final: 11 residues processed: 114 average time/residue: 0.3209 time to fit residues: 41.4230 Evaluate side-chains 104 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 63 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 129 optimal weight: 6.9990 chunk 116 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 HIS B 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.231753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158404 restraints weight = 10455.612| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.78 r_work: 0.3330 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10918 Z= 0.128 Angle : 0.492 7.566 14840 Z= 0.256 Chirality : 0.040 0.147 1760 Planarity : 0.004 0.033 1792 Dihedral : 5.272 48.436 1688 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.15 % Allowed : 11.45 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.24), residues: 1316 helix: 2.43 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.23 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.015 0.001 TYR A 451 PHE 0.026 0.001 PHE B 221 TRP 0.006 0.001 TRP B 396 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00295 (10918) covalent geometry : angle 0.49235 (14840) hydrogen bonds : bond 0.04540 ( 755) hydrogen bonds : angle 3.75314 ( 2247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 97 ASN cc_start: 0.8383 (m110) cc_final: 0.8169 (m-40) REVERT: A 212 LEU cc_start: 0.8417 (tp) cc_final: 0.7998 (mm) REVERT: A 413 MET cc_start: 0.6672 (ptp) cc_final: 0.6217 (ptm) REVERT: B 204 ILE cc_start: 0.7150 (mp) cc_final: 0.6845 (OUTLIER) REVERT: B 413 MET cc_start: 0.6630 (ptp) cc_final: 0.6183 (ptm) outliers start: 25 outliers final: 15 residues processed: 117 average time/residue: 0.3865 time to fit residues: 50.9237 Evaluate side-chains 110 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 43 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.229776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162888 restraints weight = 10652.570| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.53 r_work: 0.3482 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10918 Z= 0.138 Angle : 0.507 7.700 14840 Z= 0.264 Chirality : 0.040 0.149 1760 Planarity : 0.004 0.034 1792 Dihedral : 5.267 45.579 1688 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.81 % Allowed : 12.65 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.24), residues: 1316 helix: 2.38 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.015 0.001 TYR A 451 PHE 0.026 0.002 PHE B 221 TRP 0.006 0.001 TRP B 396 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00328 (10918) covalent geometry : angle 0.50691 (14840) hydrogen bonds : bond 0.04635 ( 755) hydrogen bonds : angle 3.77633 ( 2247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8507 (tp) cc_final: 0.8133 (mm) REVERT: A 413 MET cc_start: 0.6721 (ptp) cc_final: 0.6262 (ptm) REVERT: B 41 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7587 (ptm-80) REVERT: B 413 MET cc_start: 0.6706 (ptp) cc_final: 0.6257 (ptm) outliers start: 21 outliers final: 14 residues processed: 109 average time/residue: 0.3163 time to fit residues: 38.9057 Evaluate side-chains 112 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.229450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3854 r_free = 0.3854 target = 0.158354 restraints weight = 10614.450| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.08 r_work: 0.3427 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10918 Z= 0.134 Angle : 0.498 7.543 14840 Z= 0.260 Chirality : 0.040 0.149 1760 Planarity : 0.004 0.034 1792 Dihedral : 5.251 43.556 1688 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 12.39 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.24), residues: 1316 helix: 2.38 (0.16), residues: 1008 sheet: None (None), residues: 0 loop : -1.26 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.016 0.001 TYR A 451 PHE 0.026 0.001 PHE B 221 TRP 0.006 0.001 TRP B 396 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00314 (10918) covalent geometry : angle 0.49808 (14840) hydrogen bonds : bond 0.04580 ( 755) hydrogen bonds : angle 3.77581 ( 2247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8440 (tp) cc_final: 0.8044 (mm) REVERT: A 413 MET cc_start: 0.6729 (ptp) cc_final: 0.6228 (ptm) REVERT: B 41 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7564 (ptm-80) REVERT: B 204 ILE cc_start: 0.7143 (mp) cc_final: 0.6844 (OUTLIER) REVERT: B 237 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7094 (t) REVERT: B 413 MET cc_start: 0.6603 (ptp) cc_final: 0.6146 (ptm) outliers start: 26 outliers final: 15 residues processed: 115 average time/residue: 0.3923 time to fit residues: 50.4720 Evaluate side-chains 113 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 752 GLN Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 121 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 83 optimal weight: 0.0980 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.232471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3855 r_free = 0.3855 target = 0.161301 restraints weight = 10536.658| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.75 r_work: 0.3368 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10918 Z= 0.108 Angle : 0.472 7.326 14840 Z= 0.245 Chirality : 0.039 0.143 1760 Planarity : 0.004 0.034 1792 Dihedral : 5.138 44.068 1688 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.64 % Allowed : 13.25 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.24), residues: 1316 helix: 2.50 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -1.17 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.015 0.001 TYR A 451 PHE 0.023 0.001 PHE A 221 TRP 0.005 0.001 TRP B 396 HIS 0.001 0.000 HIS B 758 Details of bonding type rmsd covalent geometry : bond 0.00230 (10918) covalent geometry : angle 0.47217 (14840) hydrogen bonds : bond 0.04085 ( 755) hydrogen bonds : angle 3.69432 ( 2247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8409 (tp) cc_final: 0.8006 (mm) REVERT: B 41 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7445 (ptm-80) REVERT: B 204 ILE cc_start: 0.7069 (mp) cc_final: 0.6764 (OUTLIER) REVERT: B 205 LYS cc_start: 0.5591 (tptt) cc_final: 0.5298 (tppt) REVERT: B 237 VAL cc_start: 0.7267 (OUTLIER) cc_final: 0.7042 (t) REVERT: B 413 MET cc_start: 0.6560 (ptp) cc_final: 0.6172 (ptm) REVERT: B 429 MET cc_start: 0.7554 (tpt) cc_final: 0.7138 (tpt) outliers start: 19 outliers final: 12 residues processed: 110 average time/residue: 0.4041 time to fit residues: 49.9033 Evaluate side-chains 108 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 752 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 62 optimal weight: 0.0170 chunk 16 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 chunk 65 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.233563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.163849 restraints weight = 10499.100| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.72 r_work: 0.3346 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10918 Z= 0.119 Angle : 0.493 7.323 14840 Z= 0.255 Chirality : 0.039 0.156 1760 Planarity : 0.004 0.033 1792 Dihedral : 5.158 42.005 1688 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.55 % Allowed : 13.43 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.24), residues: 1316 helix: 2.45 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.015 0.001 TYR A 451 PHE 0.025 0.001 PHE B 221 TRP 0.005 0.001 TRP B 396 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00266 (10918) covalent geometry : angle 0.49276 (14840) hydrogen bonds : bond 0.04272 ( 755) hydrogen bonds : angle 3.72785 ( 2247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8406 (tp) cc_final: 0.7998 (mm) REVERT: B 41 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7556 (ptm-80) REVERT: B 204 ILE cc_start: 0.7160 (mp) cc_final: 0.6839 (OUTLIER) REVERT: B 205 LYS cc_start: 0.5612 (tptt) cc_final: 0.5308 (tppt) REVERT: B 237 VAL cc_start: 0.7227 (OUTLIER) cc_final: 0.7000 (t) REVERT: B 413 MET cc_start: 0.6584 (ptp) cc_final: 0.6181 (ptm) outliers start: 18 outliers final: 13 residues processed: 108 average time/residue: 0.4089 time to fit residues: 49.3245 Evaluate side-chains 110 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 795 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 45 optimal weight: 0.0470 chunk 68 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.233901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.161312 restraints weight = 10453.581| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.90 r_work: 0.3356 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10918 Z= 0.114 Angle : 0.484 7.289 14840 Z= 0.251 Chirality : 0.039 0.159 1760 Planarity : 0.004 0.033 1792 Dihedral : 5.133 40.712 1688 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 13.77 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1316 helix: 2.48 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -1.15 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.015 0.001 TYR A 451 PHE 0.024 0.001 PHE B 221 TRP 0.005 0.001 TRP B 396 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00251 (10918) covalent geometry : angle 0.48380 (14840) hydrogen bonds : bond 0.04163 ( 755) hydrogen bonds : angle 3.71274 ( 2247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8397 (tp) cc_final: 0.7987 (mm) REVERT: B 41 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7579 (ptm-80) REVERT: B 204 ILE cc_start: 0.7140 (mp) cc_final: 0.6824 (OUTLIER) REVERT: B 205 LYS cc_start: 0.5593 (tptt) cc_final: 0.5297 (tppt) REVERT: B 237 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.7000 (t) REVERT: B 413 MET cc_start: 0.6545 (ptp) cc_final: 0.6151 (ptm) outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 0.4072 time to fit residues: 47.9695 Evaluate side-chains 107 residues out of total 1164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 19 optimal weight: 0.0170 chunk 38 optimal weight: 0.9990 chunk 84 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 83 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 126 optimal weight: 0.0040 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.235176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.175105 restraints weight = 10647.861| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.48 r_work: 0.3571 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10918 Z= 0.100 Angle : 0.466 7.113 14840 Z= 0.240 Chirality : 0.038 0.157 1760 Planarity : 0.003 0.033 1792 Dihedral : 5.045 42.053 1688 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.29 % Allowed : 13.77 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.72 (0.24), residues: 1316 helix: 2.60 (0.16), residues: 1010 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 808 TYR 0.014 0.001 TYR A 451 PHE 0.022 0.001 PHE A 221 TRP 0.006 0.001 TRP B 396 HIS 0.001 0.000 HIS B 817 Details of bonding type rmsd covalent geometry : bond 0.00201 (10918) covalent geometry : angle 0.46564 (14840) hydrogen bonds : bond 0.03725 ( 755) hydrogen bonds : angle 3.63662 ( 2247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.69 seconds wall clock time: 74 minutes 56.24 seconds (4496.24 seconds total)