Starting phenix.real_space_refine on Sun Dec 29 22:52:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705.map" model { file = "/net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dtm_27705/12_2024/8dtm_27705_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6304 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 4129 2.51 5 N 1113 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6498 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3560 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 424} Chain breaks: 4 Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2793 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 23, 'TRANS': 316} Chain breaks: 4 Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 145 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 3.97, per 1000 atoms: 0.61 Number of scatterers: 6498 At special positions: 0 Unit cell: (89.64, 89.64, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1205 8.00 N 1113 7.00 C 4129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS C 18 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 784.3 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 12.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.564A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.716A pdb=" N LYS A 224 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.578A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.619A pdb=" N GLY A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.344A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.550A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.768A pdb=" N LEU B 500 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 646 removed outlier: 4.063A pdb=" N LEU B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 711 removed outlier: 4.006A pdb=" N LEU B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 2 through 13 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.155A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.155A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LEU A 62 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321 removed outlier: 7.648A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 471 through 473 removed outlier: 3.668A pdb=" N LYS B 584 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.889A pdb=" N PHE B 477 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.765A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.533A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 765 removed outlier: 4.318A pdb=" N GLY B 780 " --> pdb=" O GLN B 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AB6, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.640A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 885 " --> pdb=" O ARG B 852 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2125 1.35 - 1.47: 1605 1.47 - 1.59: 2861 1.59 - 1.71: 0 1.71 - 1.83: 63 Bond restraints: 6654 Sorted by residual: bond pdb=" C ARG B 759 " pdb=" N PRO B 760 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.01e-02 9.80e+03 1.06e+00 bond pdb=" CB ASP A 404 " pdb=" CG ASP A 404 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.75e-01 bond pdb=" CG LEU A 2 " pdb=" CD1 LEU A 2 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.42e-01 bond pdb=" CA ASP B 483 " pdb=" CB ASP B 483 " ideal model delta sigma weight residual 1.533 1.550 -0.017 2.15e-02 2.16e+03 6.33e-01 bond pdb=" C SER B 792 " pdb=" N PRO B 793 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.34e-01 ... (remaining 6649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 8751 1.42 - 2.84: 205 2.84 - 4.26: 42 4.26 - 5.68: 7 5.68 - 7.10: 4 Bond angle restraints: 9009 Sorted by residual: angle pdb=" C ASP B 647 " pdb=" N TYR B 648 " pdb=" CA TYR B 648 " ideal model delta sigma weight residual 122.09 116.72 5.37 1.79e+00 3.12e-01 9.00e+00 angle pdb=" C ILE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta sigma weight residual 121.62 116.98 4.64 1.83e+00 2.99e-01 6.43e+00 angle pdb=" C TYR B 633 " pdb=" N TRP B 634 " pdb=" CA TRP B 634 " ideal model delta sigma weight residual 122.37 118.19 4.18 1.72e+00 3.38e-01 5.91e+00 angle pdb=" CA GLU C 12 " pdb=" CB GLU C 12 " pdb=" CG GLU C 12 " ideal model delta sigma weight residual 114.10 118.61 -4.51 2.00e+00 2.50e-01 5.08e+00 angle pdb=" CA CYS B 797 " pdb=" CB CYS B 797 " pdb=" SG CYS B 797 " ideal model delta sigma weight residual 114.40 119.49 -5.09 2.30e+00 1.89e-01 4.89e+00 ... (remaining 9004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3496 17.75 - 35.50: 415 35.50 - 53.26: 95 53.26 - 71.01: 24 71.01 - 88.76: 11 Dihedral angle restraints: 4041 sinusoidal: 1698 harmonic: 2343 Sorted by residual: dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual -86.00 -143.51 57.51 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -28.88 -57.12 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 862 " pdb=" CB CYS B 862 " ideal model delta sinusoidal sigma weight residual 93.00 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 4038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 540 0.027 - 0.054: 244 0.054 - 0.081: 98 0.081 - 0.109: 53 0.109 - 0.136: 38 Chirality restraints: 973 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASP B 483 " pdb=" N ASP B 483 " pdb=" C ASP B 483 " pdb=" CB ASP B 483 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 970 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 634 " 0.015 2.00e-02 2.50e+03 1.90e-02 9.07e+00 pdb=" CG TRP B 634 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 634 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 634 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 634 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 634 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 634 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 634 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 634 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 634 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 483 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" CG ASP B 483 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP B 483 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 483 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 404 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP A 404 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 404 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 405 " 0.008 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 130 2.69 - 3.24: 5885 3.24 - 3.79: 9349 3.79 - 4.35: 12659 4.35 - 4.90: 21518 Nonbonded interactions: 49541 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.132 3.040 nonbonded pdb=" O SER B 880 " pdb=" OH TYR B 884 " model vdw 2.142 3.040 nonbonded pdb=" O VAL B 888 " pdb=" OG1 THR B 900 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 372 " pdb=" OD1 ASP B 533 " model vdw 2.235 3.120 nonbonded pdb=" OG SER A 339 " pdb=" O PHE A 367 " model vdw 2.262 3.040 ... (remaining 49536 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 0.027 6654 Z= 0.210 Angle : 0.564 7.103 9009 Z= 0.295 Chirality : 0.045 0.136 973 Planarity : 0.004 0.030 1162 Dihedral : 16.330 88.760 2471 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.41 % Allowed : 18.49 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 780 helix: 0.63 (0.62), residues: 73 sheet: 0.22 (0.38), residues: 196 loop : -1.04 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP B 634 HIS 0.004 0.001 HIS A 32 PHE 0.015 0.001 PHE B 703 TYR 0.010 0.001 TYR B 507 ARG 0.004 0.000 ARG A 267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.739 Fit side-chains REVERT: C 16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7381 (mtt180) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.1785 time to fit residues: 14.8298 Evaluate side-chains 57 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain B residue 816 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0970 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6654 Z= 0.190 Angle : 0.528 6.742 9009 Z= 0.277 Chirality : 0.044 0.149 973 Planarity : 0.003 0.031 1162 Dihedral : 4.629 24.463 879 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.92 % Allowed : 17.26 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.31), residues: 780 helix: 0.59 (0.59), residues: 79 sheet: 0.19 (0.37), residues: 195 loop : -1.00 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 834 HIS 0.004 0.001 HIS A 32 PHE 0.013 0.001 PHE B 707 TYR 0.010 0.001 TYR B 507 ARG 0.004 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.7351 (t-90) REVERT: B 634 TRP cc_start: 0.8808 (p90) cc_final: 0.8158 (p90) REVERT: C 16 ARG cc_start: 0.7688 (mtm180) cc_final: 0.7410 (mtt180) outliers start: 14 outliers final: 8 residues processed: 73 average time/residue: 0.1931 time to fit residues: 19.4236 Evaluate side-chains 67 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6654 Z= 0.283 Angle : 0.558 6.750 9009 Z= 0.291 Chirality : 0.045 0.144 973 Planarity : 0.004 0.030 1162 Dihedral : 4.700 24.475 876 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.60 % Allowed : 17.40 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.31), residues: 780 helix: 0.66 (0.60), residues: 79 sheet: 0.00 (0.37), residues: 197 loop : -1.02 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 251 HIS 0.005 0.001 HIS A 247 PHE 0.014 0.001 PHE B 703 TYR 0.013 0.001 TYR A 401 ARG 0.007 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 185 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7441 (t-90) REVERT: A 233 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7644 (tp) REVERT: C 16 ARG cc_start: 0.7813 (mtm180) cc_final: 0.7523 (mtt180) outliers start: 19 outliers final: 11 residues processed: 71 average time/residue: 0.1866 time to fit residues: 18.5596 Evaluate side-chains 65 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 535 ASP Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 337 ASN A 440 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6654 Z= 0.305 Angle : 0.562 6.751 9009 Z= 0.293 Chirality : 0.046 0.143 973 Planarity : 0.004 0.030 1162 Dihedral : 4.815 24.993 876 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.74 % Allowed : 17.40 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.30), residues: 780 helix: 0.46 (0.59), residues: 80 sheet: -0.09 (0.37), residues: 197 loop : -1.07 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.005 0.001 HIS A 247 PHE 0.015 0.001 PHE B 703 TYR 0.013 0.001 TYR A 401 ARG 0.004 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.790 Fit side-chains REVERT: A 74 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8053 (t0) REVERT: A 185 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7480 (t-90) REVERT: A 233 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7691 (tp) REVERT: C 16 ARG cc_start: 0.7686 (mtt180) cc_final: 0.7415 (mtm180) outliers start: 20 outliers final: 13 residues processed: 74 average time/residue: 0.1897 time to fit residues: 19.2272 Evaluate side-chains 73 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6654 Z= 0.294 Angle : 0.560 6.725 9009 Z= 0.292 Chirality : 0.045 0.151 973 Planarity : 0.004 0.030 1162 Dihedral : 4.816 25.161 876 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.42 % Allowed : 17.40 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.30), residues: 780 helix: 0.46 (0.59), residues: 80 sheet: -0.03 (0.38), residues: 192 loop : -1.14 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 834 HIS 0.004 0.001 HIS A 247 PHE 0.015 0.001 PHE B 703 TYR 0.012 0.001 TYR A 401 ARG 0.004 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.793 Fit side-chains REVERT: A 74 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8075 (t0) REVERT: A 185 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.7446 (t-90) REVERT: A 233 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7706 (tp) REVERT: C 16 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7569 (mtm180) outliers start: 25 outliers final: 18 residues processed: 80 average time/residue: 0.1968 time to fit residues: 21.3094 Evaluate side-chains 74 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 799 VAL Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.5980 chunk 76 optimal weight: 0.0270 chunk 63 optimal weight: 0.3980 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 43 optimal weight: 0.0970 chunk 55 optimal weight: 0.7980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.149 Angle : 0.505 6.561 9009 Z= 0.264 Chirality : 0.044 0.135 973 Planarity : 0.003 0.028 1162 Dihedral : 4.515 22.279 876 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.92 % Allowed : 19.18 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.31), residues: 780 helix: 0.54 (0.59), residues: 80 sheet: 0.02 (0.37), residues: 197 loop : -0.95 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 834 HIS 0.004 0.001 HIS A 32 PHE 0.013 0.001 PHE B 703 TYR 0.010 0.001 TYR B 633 ARG 0.003 0.000 ARG B 853 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.755 Fit side-chains REVERT: A 185 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.7360 (t-90) REVERT: B 821 THR cc_start: 0.8601 (m) cc_final: 0.8046 (p) outliers start: 14 outliers final: 12 residues processed: 75 average time/residue: 0.2046 time to fit residues: 20.4865 Evaluate side-chains 75 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6654 Z= 0.296 Angle : 0.553 6.565 9009 Z= 0.288 Chirality : 0.045 0.154 973 Planarity : 0.004 0.030 1162 Dihedral : 4.708 24.726 876 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.56 % Allowed : 17.95 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.30), residues: 780 helix: 0.55 (0.59), residues: 80 sheet: -0.02 (0.37), residues: 192 loop : -1.06 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 251 HIS 0.004 0.001 HIS A 247 PHE 0.015 0.001 PHE B 703 TYR 0.013 0.001 TYR A 401 ARG 0.003 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8466 (OUTLIER) cc_final: 0.8092 (t0) REVERT: A 185 HIS cc_start: 0.7820 (OUTLIER) cc_final: 0.7493 (t-90) REVERT: A 233 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7704 (tp) REVERT: B 821 THR cc_start: 0.8627 (m) cc_final: 0.8077 (p) outliers start: 26 outliers final: 22 residues processed: 82 average time/residue: 0.1935 time to fit residues: 21.6325 Evaluate side-chains 83 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 70 optimal weight: 0.0970 chunk 42 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 822 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6654 Z= 0.183 Angle : 0.510 6.635 9009 Z= 0.267 Chirality : 0.044 0.149 973 Planarity : 0.003 0.029 1162 Dihedral : 4.550 22.457 876 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.01 % Allowed : 18.49 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.30), residues: 780 helix: 0.59 (0.59), residues: 80 sheet: -0.05 (0.37), residues: 197 loop : -0.97 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 834 HIS 0.003 0.001 HIS A 32 PHE 0.014 0.001 PHE B 703 TYR 0.009 0.001 TYR B 633 ARG 0.003 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 74 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8017 (t0) REVERT: A 185 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7409 (t-90) REVERT: A 451 ARG cc_start: 0.8222 (mtt180) cc_final: 0.8002 (mtt180) outliers start: 22 outliers final: 19 residues processed: 82 average time/residue: 0.1887 time to fit residues: 21.5624 Evaluate side-chains 81 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.0470 chunk 52 optimal weight: 0.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 32 HIS B 786 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6654 Z= 0.177 Angle : 0.526 6.667 9009 Z= 0.277 Chirality : 0.044 0.146 973 Planarity : 0.003 0.028 1162 Dihedral : 4.501 21.897 876 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.01 % Allowed : 18.90 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.30), residues: 780 helix: 0.64 (0.59), residues: 80 sheet: -0.09 (0.36), residues: 197 loop : -0.94 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 834 HIS 0.005 0.001 HIS B 822 PHE 0.014 0.001 PHE B 703 TYR 0.010 0.001 TYR B 884 ARG 0.002 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7885 (ptm) cc_final: 0.7684 (ptp) REVERT: A 74 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.7949 (t0) REVERT: A 185 HIS cc_start: 0.7726 (OUTLIER) cc_final: 0.7436 (t-90) REVERT: B 822 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7161 (t-90) outliers start: 22 outliers final: 19 residues processed: 82 average time/residue: 0.1812 time to fit residues: 20.4338 Evaluate side-chains 85 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 786 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6654 Z= 0.216 Angle : 0.531 6.593 9009 Z= 0.279 Chirality : 0.044 0.148 973 Planarity : 0.003 0.031 1162 Dihedral : 4.526 22.334 876 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.29 % Allowed : 18.77 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.30), residues: 780 helix: 0.65 (0.59), residues: 80 sheet: -0.08 (0.37), residues: 197 loop : -0.96 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 834 HIS 0.003 0.001 HIS A 247 PHE 0.014 0.001 PHE B 703 TYR 0.010 0.001 TYR A 401 ARG 0.003 0.000 ARG B 875 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: A 11 MET cc_start: 0.7881 (ptm) cc_final: 0.7676 (ptp) REVERT: A 74 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8036 (t0) REVERT: A 185 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7466 (t-90) outliers start: 24 outliers final: 22 residues processed: 84 average time/residue: 0.1798 time to fit residues: 20.8239 Evaluate side-chains 86 residues out of total 730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 159 CYS Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 HIS Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 435 CYS Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 572 VAL Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 645 GLU Chi-restraints excluded: chain B residue 648 TYR Chi-restraints excluded: chain B residue 807 THR Chi-restraints excluded: chain B residue 816 ILE Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 849 VAL Chi-restraints excluded: chain C residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 64 optimal weight: 0.2980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 71 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.137241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105558 restraints weight = 9253.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109093 restraints weight = 5737.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111353 restraints weight = 4247.139| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.157 Angle : 0.509 6.512 9009 Z= 0.268 Chirality : 0.044 0.149 973 Planarity : 0.003 0.029 1162 Dihedral : 4.406 21.688 876 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.47 % Allowed : 19.73 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.31), residues: 780 helix: 0.69 (0.60), residues: 80 sheet: -0.01 (0.37), residues: 197 loop : -0.88 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 834 HIS 0.003 0.001 HIS B 867 PHE 0.014 0.001 PHE B 703 TYR 0.009 0.001 TYR B 633 ARG 0.003 0.000 ARG B 853 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1574.50 seconds wall clock time: 29 minutes 30.52 seconds (1770.52 seconds total)