Starting phenix.real_space_refine on Sun Apr 5 08:40:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mi8_48285/04_2026/9mi8_48285.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mi8_48285/04_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_48285/04_2026/9mi8_48285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mi8_48285/04_2026/9mi8_48285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mi8_48285/04_2026/9mi8_48285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mi8_48285/04_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-2.1rc1-6017/lib/python3.9/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: 1.85, per 1000 atoms: 0.21 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: 1.06 Conformation dependent library (CDL) restraints added in 182.6 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: 1.47 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: 1.72 Time building geometry restraints manager: 1.39 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=" N SER A 5 " pdb=" CA SER A 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.96e+00 bond pdb=" C VAL A 48 " pdb=" N PRO A 49 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.23e-02 6.61e+03 2.81e+00 bond pdb=" N SER A 5 " pdb=" H SER A 5 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C VAL A 272 " pdb=" N PRO A 273 " ideal model delta sigma weight residual 1.326 1.344 -0.018 1.44e-02 4.82e+03 1.55e+00 bond pdb=" C LEU A 557 " pdb=" N GLY A 558 " ideal model delta sigma weight residual 1.332 1.313 0.019 1.54e-02 4.22e+03 1.49e+00 ... (remaining 9065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 15070 1.09 - 2.19: 885 2.19 - 3.28: 94 3.28 - 4.37: 16 4.37 - 5.46: 2 Bond angle restraints: 16067 Sorted by residual: angle pdb=" C PRO A 635 " pdb=" N LYS A 636 " pdb=" CA LYS A 636 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.18e+00 angle pdb=" N ASP A 31 " pdb=" CA ASP A 31 " pdb=" CB ASP A 31 " ideal model delta sigma weight residual 113.15 109.42 3.73 1.63e+00 3.76e-01 5.23e+00 angle pdb=" N ALA A 36 " pdb=" CA ALA A 36 " pdb=" C ALA A 36 " ideal model delta sigma weight residual 108.60 111.82 -3.22 1.46e+00 4.69e-01 4.86e+00 angle pdb=" CA GLN A 759 " pdb=" CB GLN A 759 " pdb=" CG GLN A 759 " ideal model delta sigma weight residual 114.10 117.94 -3.84 2.00e+00 2.50e-01 3.68e+00 angle pdb=" CA ASP A 31 " pdb=" CB ASP A 31 " pdb=" CG ASP A 31 " ideal model delta sigma weight residual 112.60 114.52 -1.92 1.00e+00 1.00e+00 3.67e+00 ... (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: 569 0.030 - 0.061: 162 0.061 - 0.091: 43 0.091 - 0.121: 20 0.121 - 0.152: 6 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=" 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 chirality pdb=" CA ILE A 740 " pdb=" N ILE A 740 " pdb=" C ILE A 740 " pdb=" CB ILE A 740 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.960 Find NCS groups from input model: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4700 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 : 0.003 0.033 5388 Z= 0.157 Angle : 0.640 17.553 7454 Z= 0.320 Chirality : 0.035 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 covalent geometry : bond 0.00324 ( 5376) covalent geometry : angle 0.55590 ( 7442) hydrogen bonds : bond 0.25824 ( 175) hydrogen bonds : angle 7.50706 ( 441) metal coordination : bond 0.00768 ( 12) metal coordination : angle 7.90160 ( 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 : 0.227 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: 0.1737 time to fit residues: 15.2399 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 : 0.217 ------------------------------------------------------------------------------- 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: 6.9990 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: 4.9990 overall best weight: 1.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4545 r_free = 0.4545 target = 0.136610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.110304 restraints weight = 48140.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.113544 restraints weight = 21076.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.115620 restraints weight = 12650.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.116773 restraints weight = 9074.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.117628 restraints weight = 7424.562| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5388 Z= 0.150 Angle : 0.579 10.188 7454 Z= 0.304 Chirality : 0.035 0.149 800 Planarity : 0.004 0.034 779 Dihedral : 23.499 132.071 1081 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 3.25 % Allowed : 26.03 % Favored : 70.72 % 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: -1.94 (0.35), residues: 512 helix: -0.00 (0.42), residues: 141 sheet: -3.79 (0.54), residues: 63 loop : -1.35 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 282 TYR 0.007 0.001 TYR A 569 PHE 0.009 0.001 PHE A 184 TRP 0.007 0.001 TRP A 589 HIS 0.004 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 5376) covalent geometry : angle 0.54351 ( 7442) hydrogen bonds : bond 0.05074 ( 175) hydrogen bonds : angle 5.36665 ( 441) metal coordination : bond 0.01166 ( 12) metal coordination : angle 4.98879 ( 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 68 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.244 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: 0.8080 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: A 587 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7947 (ptt180) outliers start: 15 outliers final: 12 residues processed: 66 average time/residue: 0.1881 time to fit residues: 15.2491 Evaluate side-chains 62 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 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 303 VAL Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.132692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.106519 restraints weight = 48112.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.109641 restraints weight = 21271.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.111635 restraints weight = 12788.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.112909 restraints weight = 9192.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.113655 restraints weight = 7469.862| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5388 Z= 0.190 Angle : 0.618 14.258 7454 Z= 0.319 Chirality : 0.036 0.153 800 Planarity : 0.004 0.033 779 Dihedral : 23.865 125.392 1068 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.42 % Allowed : 26.25 % Favored : 68.33 % 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: -1.94 (0.36), residues: 512 helix: 0.17 (0.43), residues: 147 sheet: -3.78 (0.53), residues: 67 loop : -1.43 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 282 TYR 0.006 0.001 TYR A 618 PHE 0.008 0.001 PHE A 54 TRP 0.013 0.002 TRP A 246 HIS 0.003 0.001 HIS A 627 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 5376) covalent geometry : angle 0.56476 ( 7442) hydrogen bonds : bond 0.05615 ( 175) hydrogen bonds : angle 5.15067 ( 441) metal coordination : bond 0.00847 ( 12) metal coordination : angle 6.25742 ( 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 76 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5517 (tm-30) REVERT: A 701 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6454 (mt) REVERT: A 717 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8852 (tm-30) outliers start: 25 outliers final: 16 residues processed: 72 average time/residue: 0.1848 time to fit residues: 16.4928 Evaluate side-chains 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain A residue 352 LYS 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 701 LEU Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 0.0050 chunk 12 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.133527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.107427 restraints weight = 48188.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.110655 restraints weight = 20875.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.112709 restraints weight = 12422.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.113914 restraints weight = 8855.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.114514 restraints weight = 7228.614| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5388 Z= 0.133 Angle : 0.552 13.381 7454 Z= 0.283 Chirality : 0.034 0.144 800 Planarity : 0.003 0.033 779 Dihedral : 23.783 124.976 1065 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.69 % Allowed : 28.20 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.66 (0.36), residues: 512 helix: 0.44 (0.42), residues: 149 sheet: -3.67 (0.55), residues: 63 loop : -1.32 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 18 TYR 0.007 0.001 TYR A 344 PHE 0.009 0.001 PHE A 184 TRP 0.009 0.001 TRP A 589 HIS 0.002 0.001 HIS A 53 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5376) covalent geometry : angle 0.50635 ( 7442) hydrogen bonds : bond 0.04275 ( 175) hydrogen bonds : angle 4.77294 ( 441) metal coordination : bond 0.00775 ( 12) metal coordination : angle 5.52711 ( 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 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.231 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 717 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8727 (tm-30) REVERT: A 718 GLN cc_start: 0.9347 (tp-100) cc_final: 0.9013 (pt0) outliers start: 17 outliers final: 11 residues processed: 63 average time/residue: 0.1868 time to fit residues: 14.6163 Evaluate side-chains 58 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 267 PHE Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4487 r_free = 0.4487 target = 0.131081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.104964 restraints weight = 48079.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.108134 restraints weight = 21015.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.110103 restraints weight = 12586.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.111409 restraints weight = 9099.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.112108 restraints weight = 7344.122| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5388 Z= 0.170 Angle : 0.588 13.759 7454 Z= 0.300 Chirality : 0.035 0.152 800 Planarity : 0.004 0.033 779 Dihedral : 24.024 119.842 1065 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.99 % Allowed : 27.77 % 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: -1.72 (0.36), residues: 512 helix: 0.55 (0.42), residues: 148 sheet: -3.77 (0.53), residues: 67 loop : -1.38 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 18 TYR 0.005 0.001 TYR A 618 PHE 0.008 0.001 PHE A 184 TRP 0.013 0.002 TRP A 246 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5376) covalent geometry : angle 0.53826 ( 7442) hydrogen bonds : bond 0.05148 ( 175) hydrogen bonds : angle 4.72070 ( 441) metal coordination : bond 0.00810 ( 12) metal coordination : angle 5.93220 ( 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 72 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8826 (mmm) cc_final: 0.8489 (mmm) REVERT: A 701 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6434 (mt) REVERT: A 717 GLN cc_start: 0.9072 (tm-30) cc_final: 0.8808 (tm-30) REVERT: A 754 ASN cc_start: 0.8995 (t0) cc_final: 0.8771 (t0) outliers start: 23 outliers final: 15 residues processed: 69 average time/residue: 0.1791 time to fit residues: 15.2604 Evaluate side-chains 63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 14 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4476 r_free = 0.4476 target = 0.129724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.103790 restraints weight = 48016.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.106918 restraints weight = 20835.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.108770 restraints weight = 12472.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.110075 restraints weight = 9083.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.110949 restraints weight = 7353.271| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5388 Z= 0.204 Angle : 0.644 16.596 7454 Z= 0.326 Chirality : 0.036 0.154 800 Planarity : 0.004 0.031 779 Dihedral : 24.349 111.965 1062 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.21 % Allowed : 27.77 % Favored : 67.03 % 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: -1.93 (0.36), residues: 512 helix: 0.14 (0.42), residues: 152 sheet: -3.77 (0.53), residues: 67 loop : -1.43 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.010 0.001 TYR A 52 PHE 0.007 0.001 PHE A 184 TRP 0.014 0.002 TRP A 246 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5376) covalent geometry : angle 0.57842 ( 7442) hydrogen bonds : bond 0.05907 ( 175) hydrogen bonds : angle 4.81535 ( 441) metal coordination : bond 0.01033 ( 12) metal coordination : angle 7.05269 ( 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 71 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 47 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8769 (mmm) cc_final: 0.8465 (mmm) REVERT: A 70 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: A 322 MET cc_start: 0.8356 (tpt) cc_final: 0.8143 (tpt) REVERT: A 701 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6469 (mt) REVERT: A 717 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8831 (tm-30) REVERT: A 754 ASN cc_start: 0.8753 (t0) cc_final: 0.8434 (t0) outliers start: 24 outliers final: 19 residues processed: 65 average time/residue: 0.1946 time to fit residues: 15.4661 Evaluate side-chains 63 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 42 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU 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 158 TYR Chi-restraints excluded: chain A residue 167 ARG 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 252 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 580 GLU 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 701 LEU Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 753 ASN Chi-restraints excluded: chain A residue 767 ASN 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: 0.7980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.130509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.104617 restraints weight = 48352.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.107833 restraints weight = 20751.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.109845 restraints weight = 12363.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.111152 restraints weight = 8831.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.111954 restraints weight = 7099.638| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6709 moved from start: 0.4125 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= 0.154 Angle : 0.610 15.636 7454 Z= 0.305 Chirality : 0.035 0.157 800 Planarity : 0.004 0.032 779 Dihedral : 24.273 107.174 1061 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.69 % Allowed : 30.80 % Favored : 65.51 % 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: -1.69 (0.37), residues: 512 helix: 0.41 (0.42), residues: 155 sheet: -3.46 (0.53), residues: 73 loop : -1.33 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.007 0.001 TYR A 52 PHE 0.008 0.001 PHE A 184 TRP 0.011 0.001 TRP A 246 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5376) covalent geometry : angle 0.55367 ( 7442) hydrogen bonds : bond 0.05063 ( 175) hydrogen bonds : angle 4.54896 ( 441) metal coordination : bond 0.00867 ( 12) metal coordination : angle 6.41597 ( 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 67 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8717 (mmm) cc_final: 0.8453 (mmm) REVERT: A 322 MET cc_start: 0.8352 (tpt) cc_final: 0.8151 (tpt) REVERT: A 717 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 718 GLN cc_start: 0.9255 (tp-100) cc_final: 0.9050 (pt0) REVERT: A 754 ASN cc_start: 0.8929 (t0) cc_final: 0.8578 (t0) outliers start: 17 outliers final: 15 residues processed: 62 average time/residue: 0.1836 time to fit residues: 14.0841 Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP 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 252 LEU 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 624 ASN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 767 ASN 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: 4.9990 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.130919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.104979 restraints weight = 47730.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.108217 restraints weight = 20621.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.110168 restraints weight = 12293.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.111480 restraints weight = 8861.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.112362 restraints weight = 7160.564| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.4304 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= 0.135 Angle : 0.590 14.876 7454 Z= 0.295 Chirality : 0.035 0.161 800 Planarity : 0.004 0.031 779 Dihedral : 24.248 105.230 1061 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.69 % Allowed : 30.15 % Favored : 66.16 % 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: -1.54 (0.37), residues: 512 helix: 0.61 (0.43), residues: 155 sheet: -3.38 (0.54), residues: 69 loop : -1.31 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.007 0.001 TYR A 52 PHE 0.008 0.001 PHE A 184 TRP 0.016 0.002 TRP A 626 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5376) covalent geometry : angle 0.53770 ( 7442) hydrogen bonds : bond 0.04619 ( 175) hydrogen bonds : angle 4.42229 ( 441) metal coordination : bond 0.00800 ( 12) metal coordination : angle 6.09641 ( 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 69 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 52 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.8692 (mmm) cc_final: 0.8461 (mmm) REVERT: A 267 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7537 (m-10) REVERT: A 322 MET cc_start: 0.8303 (tpt) cc_final: 0.7523 (tmm) REVERT: A 717 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 754 ASN cc_start: 0.8924 (t0) cc_final: 0.8576 (t0) outliers start: 17 outliers final: 16 residues processed: 65 average time/residue: 0.2148 time to fit residues: 16.8693 Evaluate side-chains 68 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 ARG 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 580 GLU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.130664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.104714 restraints weight = 46826.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.107911 restraints weight = 20367.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.109801 restraints weight = 12160.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.111054 restraints weight = 8820.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.111544 restraints weight = 7187.683| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5388 Z= 0.137 Angle : 0.591 14.578 7454 Z= 0.297 Chirality : 0.035 0.168 800 Planarity : 0.003 0.031 779 Dihedral : 24.275 103.640 1061 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 4.12 % Allowed : 30.15 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.37), residues: 512 helix: 0.67 (0.43), residues: 155 sheet: -3.37 (0.52), residues: 73 loop : -1.30 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 122 TYR 0.007 0.001 TYR A 344 PHE 0.008 0.001 PHE A 184 TRP 0.010 0.001 TRP A 246 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 5376) covalent geometry : angle 0.54003 ( 7442) hydrogen bonds : bond 0.04645 ( 175) hydrogen bonds : angle 4.44702 ( 441) metal coordination : bond 0.00778 ( 12) metal coordination : angle 6.00133 ( 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 71 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7566 (m-10) REVERT: A 322 MET cc_start: 0.8177 (tpt) cc_final: 0.7405 (tmm) outliers start: 19 outliers final: 16 residues processed: 67 average time/residue: 0.2099 time to fit residues: 16.8883 Evaluate side-chains 68 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 ARG 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 288 VAL Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4493 r_free = 0.4493 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.103432 restraints weight = 48364.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.106607 restraints weight = 20767.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.108561 restraints weight = 12370.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.109915 restraints weight = 8947.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.110590 restraints weight = 7168.727| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 5388 Z= 0.186 Angle : 0.648 16.218 7454 Z= 0.324 Chirality : 0.037 0.189 800 Planarity : 0.004 0.037 779 Dihedral : 24.481 100.029 1061 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 24.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.12 % Allowed : 30.37 % Favored : 65.51 % 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: -1.73 (0.36), residues: 512 helix: 0.53 (0.43), residues: 155 sheet: -3.49 (0.51), residues: 73 loop : -1.44 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 122 TYR 0.007 0.001 TYR A 344 PHE 0.006 0.001 PHE A 638 TRP 0.016 0.002 TRP A 246 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5376) covalent geometry : angle 0.58628 ( 7442) hydrogen bonds : bond 0.05807 ( 175) hydrogen bonds : angle 4.56133 ( 441) metal coordination : bond 0.00913 ( 12) metal coordination : angle 6.92123 ( 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: 19 poor density : 48 time to evaluate : 0.231 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 70 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 267 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7681 (m-10) REVERT: A 322 MET cc_start: 0.8191 (tpt) cc_final: 0.7471 (tmm) outliers start: 19 outliers final: 16 residues processed: 64 average time/residue: 0.1943 time to fit residues: 15.3263 Evaluate side-chains 64 residues out of total 462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 GLU Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 TYR Chi-restraints excluded: chain A residue 167 ARG 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 288 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 587 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 748 LYS Chi-restraints excluded: chain A residue 767 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 49 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 8 optimal weight: 0.8980 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 734 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.131119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.105392 restraints weight = 47517.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.108625 restraints weight = 20167.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.110593 restraints weight = 11918.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.111885 restraints weight = 8521.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.112679 restraints weight = 6879.494| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.4825 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= 0.131 Angle : 0.616 14.630 7454 Z= 0.306 Chirality : 0.035 0.179 800 Planarity : 0.004 0.037 779 Dihedral : 24.388 100.988 1061 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.47 % Allowed : 30.80 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.37), residues: 512 helix: 0.84 (0.44), residues: 156 sheet: -3.53 (0.50), residues: 77 loop : -1.26 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 122 TYR 0.009 0.001 TYR A 344 PHE 0.007 0.001 PHE A 184 TRP 0.013 0.001 TRP A 626 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5376) covalent geometry : angle 0.56496 ( 7442) hydrogen bonds : bond 0.04591 ( 175) hydrogen bonds : angle 4.29151 ( 441) metal coordination : bond 0.00789 ( 12) metal coordination : angle 6.11864 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.09 seconds wall clock time: 38 minutes 17.60 seconds (2297.60 seconds total)