Starting phenix.real_space_refine on Thu Jul 2 16:26:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mi8_48285/07_2026/9mi8_48285.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 47 5.49 5 S 24 5.16 5 C 3127 2.51 5 N 894 2.21 5 O 1078 1.98 5 H 3694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8867 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 7879 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 985 Classifications: {'DNA': 48} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 47} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 247 SG CYS A 21 68.462 48.655 53.336 1.00145.54 S ATOM 298 SG CYS A 24 71.157 48.440 55.861 1.00133.29 S ATOM 776 SG CYS A 56 71.800 46.995 52.235 1.00213.30 S ATOM 1540 SG CYS A 125 57.118 20.413 58.073 1.00 41.49 S ATOM 1577 SG CYS A 128 55.961 16.997 59.293 1.00 40.07 S ATOM 2113 SG CYS A 162 56.559 17.456 55.529 1.00 43.25 S ATOM 3812 SG CYS A 295 41.685 66.251 30.002 1.00134.01 S ATOM 3850 SG CYS A 298 39.527 67.749 32.617 1.00132.98 S ATOM 4035 SG CYS A 311 42.671 65.281 33.176 1.00131.09 S ATOM 4169 SG CYS A 321 39.153 64.111 32.562 1.00142.38 S Time building chain proxies: 1.30, per 1000 atoms: 0.15 Number of scatterers: 8867 At special positions: 0 Unit cell: (88.618, 100.634, 106.642, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 24 16.00 P 47 15.00 O 1078 8.00 N 894 7.00 C 3127 6.00 H 3694 1.00 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: 0.58 Conformation dependent library (CDL) restraints added in 172.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 21 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 24 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 56 " pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" ND1 HIS A 159 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 128 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 125 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 162 " pdb=" ZN A1103 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 311 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 298 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 295 " pdb="ZN ZN A1103 " - pdb=" SG CYS A 321 " Number of angles added : 12 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 9 sheets defined 38.5% alpha, 7.7% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 removed outlier: 4.345A pdb=" N TRP A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 60 " --> pdb=" O CYS A 56 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.537A pdb=" N GLU A 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A 77 " --> pdb=" O PHE A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 77' Processing helix chain 'A' and resid 78 through 89 removed outlier: 3.593A pdb=" N GLN A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 166 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.614A pdb=" N SER A 177 " --> pdb=" O PRO A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 224 through 250 removed outlier: 3.772A pdb=" N LYS A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP A 250 " --> pdb=" O TRP A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 257 through 267 removed outlier: 4.077A pdb=" N GLU A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 290 removed outlier: 4.000A pdb=" N LEU A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.906A pdb=" N SER A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 6.298A pdb=" N LEU A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 349 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 350' Processing helix chain 'A' and resid 609 through 622 Processing helix chain 'A' and resid 702 through 723 removed outlier: 3.656A pdb=" N ILE A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 708 " --> pdb=" O ARG A 704 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A 709 " --> pdb=" O GLN A 705 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 711 " --> pdb=" O GLN A 707 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 740 removed outlier: 4.094A pdb=" N LEU A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP A 731 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 732 " --> pdb=" O GLN A 728 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG A 735 " --> pdb=" O ASP A 731 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 738 " --> pdb=" O ASN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 776 removed outlier: 3.744A pdb=" N VAL A 758 " --> pdb=" O ASN A 754 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU A 772 " --> pdb=" O LEU A 768 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 773 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 774 " --> pdb=" O ASP A 770 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 775 " --> pdb=" O ILE A 771 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 776 " --> pdb=" O GLU A 772 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 158 removed outlier: 4.116A pdb=" N ARG A 156 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 141 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 158 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 114 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA4, first strand: chain 'A' and resid 302 through 304 removed outlier: 3.581A pdb=" N VAL A 303 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR A 325 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AA6, first strand: chain 'A' and resid 547 through 548 Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 572 through 573 removed outlier: 4.175A pdb=" N PHE A 586 " --> pdb=" O GLN A 573 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 3.610A pdb=" N TRP A 589 " --> pdb=" O SER A 598 " (cutoff:3.500A) 121 hydrogen bonds defined for protein. 333 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3686 1.03 - 1.23: 91 1.23 - 1.43: 2277 1.43 - 1.62: 2979 1.62 - 1.82: 37 Bond restraints: 9070 Sorted by residual: bond pdb=" C3' DG B 47 " pdb=" C2' DG B 47 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.82e+00 bond pdb=" C3' DC B 24 " pdb=" C2' DC B 24 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.71e+00 bond pdb=" C3' DC B 34 " pdb=" C2' DC B 34 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 bond pdb=" C3' DG B 33 " pdb=" C2' DG B 33 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.22e+00 bond pdb=" C3' DT B 38 " pdb=" C2' DT B 38 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.50e+00 ... (remaining 9065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 14881 1.09 - 2.19: 1040 2.19 - 3.28: 128 3.28 - 4.37: 16 4.37 - 5.46: 2 Bond angle restraints: 16067 Sorted by residual: angle pdb=" N3 DT B 3 " pdb=" C4 DT B 3 " pdb=" O4 DT B 3 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT B 25 " pdb=" C4 DT B 25 " pdb=" O4 DT B 25 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT B 20 " pdb=" C4 DT B 20 " pdb=" O4 DT B 20 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 angle pdb=" N3 DT B 38 " pdb=" C4 DT B 38 " pdb=" O4 DT B 38 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 11 " pdb=" C4 DT B 11 " pdb=" O4 DT B 11 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 16062 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 3450 26.95 - 53.90: 454 53.90 - 80.86: 66 80.86 - 107.81: 6 107.81 - 134.76: 1 Dihedral angle restraints: 3977 sinusoidal: 2191 harmonic: 1786 Sorted by residual: dihedral pdb=" CA LYS A 305 " pdb=" C LYS A 305 " pdb=" N SER A 306 " pdb=" CA SER A 306 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" C4' DC B 40 " pdb=" C3' DC B 40 " pdb=" O3' DC B 40 " pdb=" P DT B 41 " ideal model delta sinusoidal sigma weight residual 220.00 85.24 134.76 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA ILE A 585 " pdb=" C ILE A 585 " pdb=" N PHE A 586 " pdb=" CA PHE A 586 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 3974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 491 0.030 - 0.061: 203 0.061 - 0.091: 75 0.091 - 0.121: 23 0.121 - 0.152: 8 Chirality restraints: 800 Sorted by residual: chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" C3' DG B 1 " pdb=" C4' DG B 1 " pdb=" O3' DG B 1 " pdb=" C2' DG B 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA VAL A 48 " pdb=" N VAL A 48 " pdb=" C VAL A 48 " pdb=" CB VAL A 48 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 797 not shown) Planarity restraints: 779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 31 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" CG ASP A 31 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP A 31 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP A 31 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 48 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 49 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 49 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 49 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 31 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C ASP A 31 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP A 31 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 32 " -0.007 2.00e-02 2.50e+03 ... (remaining 776 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 315 2.19 - 2.79: 13641 2.79 - 3.39: 19057 3.39 - 4.00: 25634 4.00 - 4.60: 40109 Nonbonded interactions: 98756 Sorted by model distance: nonbonded pdb=" OD2 ASP A 285 " pdb="HH21 ARG A 355 " model vdw 1.581 2.450 nonbonded pdb="HH22 ARG A 591 " pdb=" O LYS A 747 " model vdw 1.620 2.450 nonbonded pdb=" O ASN A 734 " pdb=" HG1 THR A 738 " model vdw 1.640 2.450 nonbonded pdb=" HZ3 LYS A 600 " pdb=" OP1 DT B 3 " model vdw 1.645 2.450 nonbonded pdb=" O LYS A 228 " pdb=" HG SER A 232 " model vdw 1.704 2.450 ... (remaining 98751 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: 0.460 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: 0.040 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.450 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4702 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 : 0.004 0.033 5388 Z= 0.327 Angle : 0.709 17.553 7454 Z= 0.476 Chirality : 0.040 0.152 800 Planarity : 0.004 0.037 779 Dihedral : 22.793 134.759 2140 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.16 % Favored : 89.84 % Rotamer: Outliers : 3.90 % Allowed : 27.11 % Favored : 68.98 % 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 are not related in a simple way. whole: -1.95 (0.36), residues: 512 helix: -0.02 (0.48), residues: 120 sheet: -3.90 (0.53), residues: 67 loop : -1.20 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.006 0.001 TYR A 569 PHE 0.009 0.001 PHE A 553 TRP 0.010 0.001 TRP A 589 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.33 ( 5376) covalent geometry : angle 0.63449 / 0.47 ( 7442) hydrogen bonds : bond 0.25824 / 16.66 ( 175) hydrogen bonds : angle 7.50706 / 5.08 ( 441) metal coordination : bond 0.00768 / 0.46 ( 12) metal coordination : angle 7.90160 / 4.36 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.192 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 612 GLU cc_start: 0.9576 (tp30) cc_final: 0.9318 (tm-30) REVERT: A 767 ASN cc_start: 0.9221 (m110) cc_final: 0.9019 (t0) outliers start: 18 outliers final: 16 residues processed: 70 average time/residue: 0.1347 time to fit residues: 11.8781 Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 554 SER Chi-restraints excluded: chain A residue 599 ASN Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 714 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 53 optimal weight: 9.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 GLN A 326 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.136979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.110654 restraints weight = 47698.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.113743 restraints weight = 20826.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.115887 restraints weight = 12592.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.117157 restraints weight = 8966.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.117967 restraints weight = 7188.726| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5388 Z= 0.174 Angle : 0.645 11.241 7454 Z= 0.353 Chirality : 0.037 0.153 800 Planarity : 0.004 0.034 779 Dihedral : 23.604 135.049 1081 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 4.34 % Allowed : 26.25 % Favored : 69.41 % 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 are not related in a simple way. whole: -2.02 (0.35), residues: 512 helix: -0.19 (0.41), residues: 138 sheet: -3.74 (0.54), residues: 67 loop : -1.31 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 704 TYR 0.009 0.001 TYR A 618 PHE 0.010 0.001 PHE A 54 TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 ( 5376) covalent geometry : angle 0.60138 / 0.35 ( 7442) hydrogen bonds : bond 0.06825 / 4.61 ( 175) hydrogen bonds : angle 6.12398 / 4.22 ( 441) metal coordination : bond 0.01121 / 0.79 ( 12) metal coordination : angle 5.84602 / 3.17 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.140 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 267 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7412 (m-10) REVERT: A 602 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: A 612 GLU cc_start: 0.8935 (tp30) cc_final: 0.8714 (tm-30) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.1313 time to fit residues: 11.2871 Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 247 ASN Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 602 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.135798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.109584 restraints weight = 47130.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.112733 restraints weight = 20581.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.114739 restraints weight = 12310.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.115985 restraints weight = 8783.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.116861 restraints weight = 7093.909| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5388 Z= 0.188 Angle : 0.611 10.218 7454 Z= 0.337 Chirality : 0.037 0.154 800 Planarity : 0.004 0.034 779 Dihedral : 23.705 131.660 1068 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.69 % Allowed : 27.77 % Favored : 68.55 % 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 are not related in a simple way. whole: -2.08 (0.35), residues: 512 helix: -0.26 (0.41), residues: 138 sheet: -3.81 (0.54), residues: 67 loop : -1.31 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.007 0.001 TYR A 618 PHE 0.007 0.001 PHE A 54 TRP 0.016 0.002 TRP A 626 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 ( 5376) covalent geometry : angle 0.57548 / 0.33 ( 7442) hydrogen bonds : bond 0.06701 / 4.58 ( 175) hydrogen bonds : angle 5.92009 / 4.12 ( 441) metal coordination : bond 0.00975 / 0.61 ( 12) metal coordination : angle 5.14126 / 2.75 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.144 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: A 267 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7451 (m-10) outliers start: 17 outliers final: 13 residues processed: 64 average time/residue: 0.1362 time to fit residues: 11.0480 Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.135590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.109282 restraints weight = 48600.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.112473 restraints weight = 21192.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.114556 restraints weight = 12649.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.115813 restraints weight = 8999.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.116582 restraints weight = 7248.675| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6484 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5388 Z= 0.151 Angle : 0.586 10.949 7454 Z= 0.320 Chirality : 0.036 0.151 800 Planarity : 0.004 0.035 779 Dihedral : 23.765 130.787 1065 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.47 % Allowed : 29.28 % Favored : 67.25 % 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 are not related in a simple way. whole: -1.98 (0.35), residues: 512 helix: -0.22 (0.41), residues: 140 sheet: -3.74 (0.54), residues: 67 loop : -1.24 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.009 0.001 TYR A 618 PHE 0.007 0.001 PHE A 184 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 ( 5376) covalent geometry : angle 0.55008 / 0.32 ( 7442) hydrogen bonds : bond 0.05346 / 3.69 ( 175) hydrogen bonds : angle 5.55397 / 3.87 ( 441) metal coordination : bond 0.00893 / 0.58 ( 12) metal coordination : angle 5.05630 / 2.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.136 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 267 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: A 701 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6337 (mt) REVERT: A 717 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8640 (tm-30) outliers start: 16 outliers final: 12 residues processed: 62 average time/residue: 0.1189 time to fit residues: 9.3809 Evaluate side-chains 60 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 352 LYS Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 701 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.135867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.109573 restraints weight = 47967.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.112752 restraints weight = 20874.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.114732 restraints weight = 12462.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.116051 restraints weight = 8970.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.116696 restraints weight = 7203.210| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5388 Z= 0.129 Angle : 0.557 10.735 7454 Z= 0.303 Chirality : 0.036 0.146 800 Planarity : 0.004 0.035 779 Dihedral : 23.780 129.866 1063 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.04 % Allowed : 30.15 % Favored : 66.81 % 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 are not related in a simple way. whole: -1.80 (0.36), residues: 512 helix: -0.05 (0.41), residues: 141 sheet: -3.67 (0.56), residues: 63 loop : -1.18 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 704 TYR 0.013 0.001 TYR A 344 PHE 0.008 0.001 PHE A 184 TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 ( 5376) covalent geometry : angle 0.52400 / 0.30 ( 7442) hydrogen bonds : bond 0.04909 / 3.39 ( 175) hydrogen bonds : angle 5.29372 / 3.70 ( 441) metal coordination : bond 0.00818 / 0.54 ( 12) metal coordination : angle 4.76558 / 2.54 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7524 (m-10) REVERT: A 602 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: A 701 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6298 (mt) REVERT: A 717 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8655 (tm-30) REVERT: A 718 GLN cc_start: 0.9217 (tp-100) cc_final: 0.8994 (pt0) outliers start: 14 outliers final: 10 residues processed: 57 average time/residue: 0.1242 time to fit residues: 8.9860 Evaluate side-chains 57 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.133657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.107462 restraints weight = 48102.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.110573 restraints weight = 21124.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.112566 restraints weight = 12683.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.113865 restraints weight = 9117.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.114494 restraints weight = 7333.344| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5388 Z= 0.175 Angle : 0.587 11.459 7454 Z= 0.318 Chirality : 0.037 0.153 800 Planarity : 0.004 0.034 779 Dihedral : 23.890 126.547 1063 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.12 % Allowed : 29.07 % Favored : 66.81 % 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 are not related in a simple way. whole: -1.91 (0.36), residues: 512 helix: 0.03 (0.42), residues: 142 sheet: -3.77 (0.53), residues: 67 loop : -1.29 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.011 0.001 TYR A 618 PHE 0.007 0.001 PHE A 184 TRP 0.013 0.001 TRP A 246 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.17 ( 5376) covalent geometry : angle 0.54775 / 0.31 ( 7442) hydrogen bonds : bond 0.05654 / 3.96 ( 175) hydrogen bonds : angle 5.24107 / 3.63 ( 441) metal coordination : bond 0.00836 / 0.51 ( 12) metal coordination : angle 5.28622 / 2.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 66 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8072 (ptt180) REVERT: A 701 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6371 (mt) REVERT: A 717 GLN cc_start: 0.8950 (tm-30) cc_final: 0.8675 (tm-30) outliers start: 19 outliers final: 14 residues processed: 64 average time/residue: 0.1205 time to fit residues: 9.7769 Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 243 ASP Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 701 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 627 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.134672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.108443 restraints weight = 47799.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.111599 restraints weight = 20711.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.113639 restraints weight = 12339.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.114819 restraints weight = 8829.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.115714 restraints weight = 7191.722| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5388 Z= 0.131 Angle : 0.552 11.242 7454 Z= 0.300 Chirality : 0.036 0.148 800 Planarity : 0.003 0.034 779 Dihedral : 23.890 126.532 1063 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.04 % Allowed : 29.28 % Favored : 67.68 % 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 are not related in a simple way. whole: -1.70 (0.36), residues: 512 helix: 0.31 (0.42), residues: 144 sheet: -3.75 (0.55), residues: 63 loop : -1.24 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 704 TYR 0.004 0.001 TYR A 618 PHE 0.021 0.001 PHE A 339 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.13 ( 5376) covalent geometry : angle 0.51551 / 0.30 ( 7442) hydrogen bonds : bond 0.04694 / 3.29 ( 175) hydrogen bonds : angle 5.08794 / 3.53 ( 441) metal coordination : bond 0.00762 / 0.49 ( 12) metal coordination : angle 4.94569 / 2.64 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: A 701 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6318 (mt) REVERT: A 717 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8647 (tm-30) outliers start: 14 outliers final: 11 residues processed: 59 average time/residue: 0.1225 time to fit residues: 9.2142 Evaluate side-chains 59 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 718 GLN A 734 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.134851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.108705 restraints weight = 47464.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.111860 restraints weight = 20558.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.113860 restraints weight = 12268.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.115086 restraints weight = 8783.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.115587 restraints weight = 7137.602| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5388 Z= 0.127 Angle : 0.550 11.145 7454 Z= 0.296 Chirality : 0.036 0.150 800 Planarity : 0.003 0.033 779 Dihedral : 23.899 125.384 1063 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 3.47 % Allowed : 28.85 % Favored : 67.68 % 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 are not related in a simple way. whole: -1.63 (0.36), residues: 512 helix: 0.46 (0.42), residues: 149 sheet: -3.72 (0.55), residues: 63 loop : -1.28 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 282 TYR 0.017 0.001 TYR A 344 PHE 0.013 0.001 PHE A 57 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.13 ( 5376) covalent geometry : angle 0.51489 / 0.29 ( 7442) hydrogen bonds : bond 0.04521 / 3.18 ( 175) hydrogen bonds : angle 4.91753 / 3.40 ( 441) metal coordination : bond 0.00764 / 0.50 ( 12) metal coordination : angle 4.85323 / 2.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8114 (OUTLIER) cc_final: 0.7557 (m-10) REVERT: A 602 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: A 701 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6300 (mt) REVERT: A 717 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8594 (tm-30) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.1521 time to fit residues: 11.3782 Evaluate side-chains 61 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 62 HIS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.0670 overall best weight: 0.8924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.134465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.108220 restraints weight = 47192.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.111407 restraints weight = 20472.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.113392 restraints weight = 12229.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.114656 restraints weight = 8777.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.115562 restraints weight = 7092.054| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5388 Z= 0.134 Angle : 0.558 11.271 7454 Z= 0.302 Chirality : 0.036 0.153 800 Planarity : 0.003 0.033 779 Dihedral : 23.915 124.501 1063 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.25 % Allowed : 29.93 % Favored : 66.81 % 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 are not related in a simple way. whole: -1.61 (0.36), residues: 512 helix: 0.51 (0.43), residues: 149 sheet: -3.74 (0.54), residues: 63 loop : -1.28 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.011 0.001 TYR A 52 PHE 0.009 0.001 PHE A 57 TRP 0.009 0.002 TRP A 246 HIS 0.002 0.001 HIS A 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 5376) covalent geometry : angle 0.52228 / 0.30 ( 7442) hydrogen bonds : bond 0.04658 / 3.28 ( 175) hydrogen bonds : angle 4.88703 / 3.37 ( 441) metal coordination : bond 0.00738 / 0.48 ( 12) metal coordination : angle 4.90725 / 2.62 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.6466 (mmp) cc_final: 0.5853 (mmm) REVERT: A 267 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7512 (m-10) REVERT: A 287 MET cc_start: 0.4415 (OUTLIER) cc_final: 0.3699 (mpp) REVERT: A 602 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: A 701 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6293 (mt) REVERT: A 717 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8601 (tm-30) REVERT: A 718 GLN cc_start: 0.9322 (tp40) cc_final: 0.9086 (pt0) outliers start: 15 outliers final: 11 residues processed: 58 average time/residue: 0.1304 time to fit residues: 9.5308 Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.134883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.108555 restraints weight = 47731.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.111777 restraints weight = 20465.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.113763 restraints weight = 12154.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.115086 restraints weight = 8737.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.115946 restraints weight = 7037.371| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5388 Z= 0.125 Angle : 0.555 11.403 7454 Z= 0.299 Chirality : 0.036 0.154 800 Planarity : 0.003 0.033 779 Dihedral : 23.928 123.771 1063 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.69 % Allowed : 28.85 % Favored : 67.46 % 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 are not related in a simple way. whole: -1.55 (0.37), residues: 512 helix: 0.58 (0.43), residues: 149 sheet: -3.73 (0.54), residues: 63 loop : -1.24 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.011 0.001 TYR A 52 PHE 0.009 0.001 PHE A 57 TRP 0.016 0.002 TRP A 626 HIS 0.005 0.001 HIS A 627 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 5376) covalent geometry : angle 0.51942 / 0.30 ( 7442) hydrogen bonds : bond 0.04513 / 3.19 ( 175) hydrogen bonds : angle 4.78208 / 3.30 ( 441) metal coordination : bond 0.00727 / 0.47 ( 12) metal coordination : angle 4.90817 / 2.62 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 762 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7468 (m-10) REVERT: A 282 ARG cc_start: 0.6784 (mmt90) cc_final: 0.5845 (mmt90) REVERT: A 602 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: A 701 LEU cc_start: 0.6528 (OUTLIER) cc_final: 0.6279 (mt) REVERT: A 717 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 718 GLN cc_start: 0.9312 (tp40) cc_final: 0.9010 (pt0) outliers start: 17 outliers final: 13 residues processed: 62 average time/residue: 0.1713 time to fit residues: 13.1272 Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 116 GLU Chi-restraints excluded: chain A residue 172 PHE Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 748 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.135141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.108914 restraints weight = 47509.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.112130 restraints weight = 20447.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.114095 restraints weight = 12213.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.115416 restraints weight = 8822.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.116341 restraints weight = 7100.107| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5388 Z= 0.121 Angle : 0.558 11.305 7454 Z= 0.299 Chirality : 0.036 0.157 800 Planarity : 0.003 0.033 779 Dihedral : 23.942 122.834 1063 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.47 % Allowed : 29.28 % Favored : 67.25 % 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 are not related in a simple way. whole: -1.44 (0.37), residues: 512 helix: 0.73 (0.43), residues: 149 sheet: -3.69 (0.54), residues: 63 loop : -1.20 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 122 TYR 0.018 0.001 TYR A 344 PHE 0.009 0.001 PHE A 184 TRP 0.013 0.001 TRP A 626 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 5376) covalent geometry : angle 0.52346 / 0.30 ( 7442) hydrogen bonds : bond 0.04393 / 3.11 ( 175) hydrogen bonds : angle 4.66024 / 3.20 ( 441) metal coordination : bond 0.00715 / 0.47 ( 12) metal coordination : angle 4.86070 / 2.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1673.93 seconds wall clock time: 29 minutes 9.02 seconds (1749.02 seconds total)