Starting phenix.real_space_refine on Wed Aug 5 12:02:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.map" model { file = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ywh_39633/08_2026/8ywh_39633.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 141 5.49 5 S 9 5.16 5 C 5801 2.51 5 N 1750 2.21 5 O 2256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9957 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6993 Classifications: {'peptide': 845} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 824} Chain breaks: 1 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2085 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 8, 'rna3p_pur': 43, 'rna3p_pyr': 39} Link IDs: {'rna2p': 16, 'rna3p': 81} Chain: "C" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 630 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "D" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Time building chain proxies: 1.62, per 1000 atoms: 0.16 Number of scatterers: 9957 At special positions: 0 Unit cell: (86.775, 105.3, 139.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 P 141 15.00 O 2256 8.00 N 1750 7.00 C 5801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 151.7 milliseconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1610 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 6 sheets defined 49.0% alpha, 12.5% beta 37 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 40 through 74 removed outlier: 3.909A pdb=" N ASN A 44 " --> pdb=" O ASN A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.649A pdb=" N GLU A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 124 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 119 through 124' Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.809A pdb=" N SER A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.936A pdb=" N ARG A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.301A pdb=" N ALA A 189 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.577A pdb=" N ILE A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 Processing helix chain 'A' and resid 250 through 265 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.531A pdb=" N ILE A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.790A pdb=" N ILE A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.723A pdb=" N ASN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 386 Processing helix chain 'A' and resid 396 through 408 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.844A pdb=" N ASP A 442 " --> pdb=" O THR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 Processing helix chain 'A' and resid 481 through 500 removed outlier: 3.668A pdb=" N ALA A 485 " --> pdb=" O GLY A 481 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 531 through 549 Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.663A pdb=" N LYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 660 through 665 removed outlier: 3.762A pdb=" N HIS A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 681 removed outlier: 4.270A pdb=" N TYR A 670 " --> pdb=" O ASP A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 695 removed outlier: 3.609A pdb=" N LYS A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 730 Processing helix chain 'A' and resid 776 through 788 removed outlier: 3.503A pdb=" N LYS A 787 " --> pdb=" O ALA A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 Processing sheet with id=AA1, first strand: chain 'A' and resid 505 through 507 removed outlier: 3.616A pdb=" N ASP A 473 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 11 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL A 16 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL A 33 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 18 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA A 31 " --> pdb=" O TYR A 18 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 20 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.707A pdb=" N SER A 246 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 713 through 719 removed outlier: 4.118A pdb=" N ILE A 634 " --> pdb=" O GLY A 717 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 719 " --> pdb=" O THR A 632 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR A 632 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N SER A 623 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASN A 637 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N LEU A 621 " --> pdb=" O ASN A 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 755 through 762 removed outlier: 3.675A pdb=" N ALA A 797 " --> pdb=" O VAL A 749 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU A 751 " --> pdb=" O PHE A 795 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE A 795 " --> pdb=" O LEU A 751 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 766 through 769 Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 852 removed outlier: 4.587A pdb=" N ILE A 849 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG A 824 " --> pdb=" O ASN A 818 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN A 828 " --> pdb=" O VAL A 814 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL A 814 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 804 " --> pdb=" O TYR A 863 " (cutoff:3.500A) 326 hydrogen bonds defined for protein. 951 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 91 hydrogen bonds 182 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2211 1.33 - 1.45: 2813 1.45 - 1.57: 5110 1.57 - 1.69: 279 1.69 - 1.81: 16 Bond restraints: 10429 Sorted by residual: bond pdb=" C3' DC C 14 " pdb=" C2' DC C 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG D 41 " pdb=" O3' DG D 41 " ideal model delta sigma weight residual 1.435 1.399 0.036 1.30e-02 5.92e+03 7.56e+00 bond pdb=" C1' DT D 45 " pdb=" N1 DT D 45 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.18e+00 bond pdb=" C3' DC C 32 " pdb=" O3' DC C 32 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.83e+00 bond pdb=" C1' DT D 36 " pdb=" N1 DT D 36 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.47e+00 ... (remaining 10424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 13993 1.89 - 3.77: 659 3.77 - 5.66: 38 5.66 - 7.54: 11 7.54 - 9.43: 4 Bond angle restraints: 14705 Sorted by residual: angle pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sigma weight residual 117.70 123.39 -5.69 1.20e+00 6.94e-01 2.25e+01 angle pdb=" O5' G B 43 " pdb=" C5' G B 43 " pdb=" C4' G B 43 " ideal model delta sigma weight residual 109.40 113.09 -3.69 8.00e-01 1.56e+00 2.12e+01 angle pdb=" C1' G B 43 " pdb=" N9 G B 43 " pdb=" C4 G B 43 " ideal model delta sigma weight residual 126.50 132.09 -5.59 1.30e+00 5.92e-01 1.85e+01 angle pdb=" N3 DT D 45 " pdb=" C4 DT D 45 " pdb=" O4 DT D 45 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT D 36 " pdb=" C4 DT D 36 " pdb=" O4 DT D 36 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 14700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 5675 35.86 - 71.73: 629 71.73 - 107.59: 48 107.59 - 143.45: 0 143.45 - 179.31: 3 Dihedral angle restraints: 6355 sinusoidal: 3849 harmonic: 2506 Sorted by residual: dihedral pdb=" O4' U B 4 " pdb=" C1' U B 4 " pdb=" N1 U B 4 " pdb=" C2 U B 4 " ideal model delta sinusoidal sigma weight residual -160.00 17.90 -177.90 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' A B 65 " pdb=" C1' A B 65 " pdb=" N9 A B 65 " pdb=" C4 A B 65 " ideal model delta sinusoidal sigma weight residual -106.00 -173.14 67.14 1 1.70e+01 3.46e-03 2.03e+01 dihedral pdb=" CA GLU A 794 " pdb=" C GLU A 794 " pdb=" N PHE A 795 " pdb=" CA PHE A 795 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 6352 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1211 0.044 - 0.088: 291 0.088 - 0.132: 157 0.132 - 0.177: 44 0.177 - 0.221: 3 Chirality restraints: 1706 Sorted by residual: chirality pdb=" C3' A B 64 " pdb=" C4' A B 64 " pdb=" O3' A B 64 " pdb=" C2' A B 64 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE A 475 " pdb=" CA ILE A 475 " pdb=" CG1 ILE A 475 " pdb=" CG2 ILE A 475 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LYS A 422 " pdb=" N LYS A 422 " pdb=" C LYS A 422 " pdb=" CB LYS A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.85e-01 ... (remaining 1703 not shown) Planarity restraints: 1364 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A B 53 " -0.034 2.00e-02 2.50e+03 1.54e-02 6.55e+00 pdb=" N9 A B 53 " 0.033 2.00e-02 2.50e+03 pdb=" C8 A B 53 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A B 53 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A B 53 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A B 53 " -0.011 2.00e-02 2.50e+03 pdb=" N1 A B 53 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A B 53 " 0.001 2.00e-02 2.50e+03 pdb=" C4 A B 53 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 54 " -0.029 2.00e-02 2.50e+03 1.36e-02 5.08e+00 pdb=" N9 A B 54 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A B 54 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A B 54 " -0.003 2.00e-02 2.50e+03 pdb=" C5 A B 54 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A B 54 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A B 54 " -0.007 2.00e-02 2.50e+03 pdb=" N1 A B 54 " -0.007 2.00e-02 2.50e+03 pdb=" C2 A B 54 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A B 54 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A B 54 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A B 52 " 0.029 2.00e-02 2.50e+03 1.28e-02 4.53e+00 pdb=" N9 A B 52 " -0.028 2.00e-02 2.50e+03 pdb=" C8 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A B 52 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A B 52 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A B 52 " 0.007 2.00e-02 2.50e+03 pdb=" N6 A B 52 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A B 52 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A B 52 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A B 52 " -0.006 2.00e-02 2.50e+03 pdb=" C4 A B 52 " -0.002 2.00e-02 2.50e+03 ... (remaining 1361 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1297 2.74 - 3.28: 9288 3.28 - 3.82: 18384 3.82 - 4.36: 22406 4.36 - 4.90: 34436 Nonbonded interactions: 85811 Sorted by model distance: nonbonded pdb=" OE2 GLU A 322 " pdb=" O2' A B 8 " model vdw 2.205 3.040 nonbonded pdb=" NZ LYS A 700 " pdb=" O2 C B 32 " model vdw 2.225 3.120 nonbonded pdb=" NH2 ARG A 48 " pdb=" OP2 U B 15 " model vdw 2.227 3.120 nonbonded pdb=" NE2 GLN A 433 " pdb=" OE1 GLU A 435 " model vdw 2.227 3.120 nonbonded pdb=" OD2 ASP A 261 " pdb=" NH1 ARG A 314 " model vdw 2.247 3.120 ... (remaining 85806 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 10429 Z= 0.328 Angle : 0.820 9.426 14705 Z= 0.582 Chirality : 0.052 0.221 1706 Planarity : 0.004 0.038 1364 Dihedral : 24.041 179.313 4745 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 6.22 % Allowed : 38.60 % Favored : 55.18 % 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: 0.08 (0.28), residues: 841 helix: 0.60 (0.26), residues: 365 sheet: -0.46 (0.66), residues: 59 loop : -0.24 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 734 TYR 0.028 0.002 TYR A 670 PHE 0.029 0.002 PHE A 758 TRP 0.011 0.002 TRP A 408 HIS 0.005 0.001 HIS A 879 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.33 (10429) covalent geometry : angle 0.81969 / 0.58 (14705) hydrogen bonds : bond 0.19705 / 13.50 ( 417) hydrogen bonds : angle 6.94984 / 4.90 ( 1133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 85 time to evaluate : 0.323 Fit side-chains REVERT: A 59 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.7406 (mtt180) REVERT: A 199 ASP cc_start: 0.7694 (m-30) cc_final: 0.7484 (m-30) REVERT: A 366 GLU cc_start: 0.7066 (tp30) cc_final: 0.6741 (tp30) REVERT: A 380 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7814 (mp) REVERT: A 505 LYS cc_start: 0.7647 (mppt) cc_final: 0.7068 (mmmt) REVERT: A 549 LYS cc_start: 0.2903 (OUTLIER) cc_final: 0.1655 (mppt) REVERT: A 611 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8643 (tmtt) REVERT: A 615 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: A 619 ASP cc_start: 0.7987 (t0) cc_final: 0.7606 (m-30) REVERT: A 629 LYS cc_start: 0.6950 (mttt) cc_final: 0.6699 (mmtp) REVERT: A 645 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.6034 (m-30) REVERT: A 648 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7525 (mtmm) REVERT: A 729 ASP cc_start: 0.8391 (m-30) cc_final: 0.8040 (m-30) REVERT: A 782 GLU cc_start: 0.7891 (tp30) cc_final: 0.7517 (tt0) REVERT: A 785 LYS cc_start: 0.7479 (mttp) cc_final: 0.7247 (mmtp) outliers start: 48 outliers final: 23 residues processed: 120 average time/residue: 0.5633 time to fit residues: 72.8075 Evaluate side-chains 101 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 615 GLU Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Chi-restraints excluded: chain A residue 883 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 370 ASN A 413 ASN A 419 ASN ** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.193279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158515 restraints weight = 10207.110| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.59 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10429 Z= 0.159 Angle : 0.639 8.566 14705 Z= 0.350 Chirality : 0.044 0.289 1706 Planarity : 0.004 0.027 1364 Dihedral : 23.907 179.654 2978 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 9.33 % Allowed : 34.20 % Favored : 56.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.28), residues: 841 helix: 1.01 (0.26), residues: 376 sheet: -0.37 (0.60), residues: 69 loop : -0.14 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 494 TYR 0.016 0.002 TYR A 670 PHE 0.014 0.002 PHE A 747 TRP 0.004 0.001 TRP A 229 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (10429) covalent geometry : angle 0.63911 / 0.35 (14705) hydrogen bonds : bond 0.06198 / 4.32 ( 417) hydrogen bonds : angle 4.74020 / 3.37 ( 1133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 85 time to evaluate : 0.308 Fit side-chains REVERT: A 114 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7767 (tptt) REVERT: A 380 ILE cc_start: 0.7742 (OUTLIER) cc_final: 0.7481 (mp) REVERT: A 502 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7068 (pp) REVERT: A 524 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5961 (mtmt) REVERT: A 533 HIS cc_start: 0.6503 (OUTLIER) cc_final: 0.6280 (t70) REVERT: A 619 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6761 (m-30) REVERT: A 625 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.8255 (mmt-90) REVERT: A 629 LYS cc_start: 0.6859 (mttt) cc_final: 0.6643 (mmtp) REVERT: A 645 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5802 (m-30) REVERT: A 729 ASP cc_start: 0.8169 (m-30) cc_final: 0.7826 (m-30) REVERT: A 848 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7053 (ttp80) outliers start: 72 outliers final: 25 residues processed: 143 average time/residue: 0.4749 time to fit residues: 73.5481 Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 74 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 645 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 812 TYR Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 69 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 54 optimal weight: 0.0970 chunk 35 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 282 GLN A 365 GLN A 370 ASN A 419 ASN A 637 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.186677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.151481 restraints weight = 10183.974| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.60 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10429 Z= 0.246 Angle : 0.707 8.784 14705 Z= 0.379 Chirality : 0.048 0.294 1706 Planarity : 0.006 0.060 1364 Dihedral : 23.921 179.966 2944 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 9.97 % Allowed : 32.25 % Favored : 57.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.28), residues: 841 helix: 0.95 (0.26), residues: 376 sheet: -0.50 (0.60), residues: 69 loop : -0.26 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 734 TYR 0.017 0.002 TYR A 730 PHE 0.022 0.002 PHE A 758 TRP 0.011 0.002 TRP A 229 HIS 0.006 0.001 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (10429) covalent geometry : angle 0.70693 / 0.38 (14705) hydrogen bonds : bond 0.06214 / 4.26 ( 417) hydrogen bonds : angle 4.55154 / 3.27 ( 1133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 78 time to evaluate : 0.219 Fit side-chains REVERT: A 114 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8161 (tptt) REVERT: A 163 GLU cc_start: 0.7850 (pt0) cc_final: 0.7538 (pt0) REVERT: A 292 LYS cc_start: 0.6553 (mmtp) cc_final: 0.5948 (mptt) REVERT: A 619 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: A 705 ASP cc_start: 0.6623 (m-30) cc_final: 0.6398 (m-30) REVERT: A 729 ASP cc_start: 0.8177 (m-30) cc_final: 0.7828 (m-30) REVERT: A 768 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (ttpp) REVERT: A 848 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7315 (ttp80) outliers start: 77 outliers final: 40 residues processed: 143 average time/residue: 0.3663 time to fit residues: 57.6747 Evaluate side-chains 117 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 88 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 81 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 282 GLN A 370 ASN A 637 ASN A 685 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.191070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156153 restraints weight = 10254.879| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.60 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10429 Z= 0.141 Angle : 0.597 15.247 14705 Z= 0.323 Chirality : 0.041 0.295 1706 Planarity : 0.004 0.028 1364 Dihedral : 23.766 179.836 2934 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 8.55 % Allowed : 33.42 % Favored : 58.03 % 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: 0.58 (0.28), residues: 841 helix: 1.23 (0.26), residues: 376 sheet: -0.33 (0.62), residues: 69 loop : -0.22 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 625 TYR 0.015 0.001 TYR A 358 PHE 0.015 0.002 PHE A 758 TRP 0.007 0.001 TRP A 229 HIS 0.003 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (10429) covalent geometry : angle 0.59653 / 0.32 (14705) hydrogen bonds : bond 0.04863 / 3.35 ( 417) hydrogen bonds : angle 4.33473 / 3.10 ( 1133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 77 time to evaluate : 0.317 Fit side-chains REVERT: A 292 LYS cc_start: 0.6562 (mmtp) cc_final: 0.6002 (mptt) REVERT: A 619 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: A 729 ASP cc_start: 0.8030 (m-30) cc_final: 0.7737 (m-30) REVERT: A 768 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7833 (ttpp) REVERT: A 848 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7224 (ttp80) outliers start: 66 outliers final: 33 residues processed: 130 average time/residue: 0.4163 time to fit residues: 58.9825 Evaluate side-chains 103 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 120 ASN Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 359 GLN A 370 ASN A 419 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 HIS A 668 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.188708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154107 restraints weight = 10144.900| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.55 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10429 Z= 0.180 Angle : 0.618 13.145 14705 Z= 0.333 Chirality : 0.043 0.295 1706 Planarity : 0.004 0.045 1364 Dihedral : 23.658 179.972 2930 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 8.94 % Allowed : 33.29 % Favored : 57.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 841 helix: 1.25 (0.26), residues: 376 sheet: -0.18 (0.64), residues: 69 loop : -0.24 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 734 TYR 0.016 0.002 TYR A 812 PHE 0.018 0.002 PHE A 758 TRP 0.010 0.001 TRP A 229 HIS 0.008 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (10429) covalent geometry : angle 0.61819 / 0.33 (14705) hydrogen bonds : bond 0.04992 / 3.44 ( 417) hydrogen bonds : angle 4.26859 / 3.06 ( 1133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 73 time to evaluate : 0.293 Fit side-chains REVERT: A 99 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.6975 (tttt) REVERT: A 292 LYS cc_start: 0.6655 (mmtp) cc_final: 0.6135 (mptt) REVERT: A 619 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: A 729 ASP cc_start: 0.8078 (m-30) cc_final: 0.7761 (m-30) REVERT: A 768 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7899 (ttpp) REVERT: A 848 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7382 (ttp80) outliers start: 69 outliers final: 39 residues processed: 134 average time/residue: 0.4041 time to fit residues: 59.1030 Evaluate side-chains 111 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 370 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.190575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.157431 restraints weight = 10165.769| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.46 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10429 Z= 0.145 Angle : 0.579 12.509 14705 Z= 0.316 Chirality : 0.041 0.296 1706 Planarity : 0.004 0.031 1364 Dihedral : 23.569 179.924 2930 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.90 % Allowed : 34.07 % Favored : 58.03 % 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: 0.73 (0.28), residues: 841 helix: 1.37 (0.26), residues: 376 sheet: -0.14 (0.64), residues: 69 loop : -0.18 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.016 0.001 TYR A 358 PHE 0.016 0.001 PHE A 758 TRP 0.008 0.001 TRP A 229 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (10429) covalent geometry : angle 0.57931 / 0.32 (14705) hydrogen bonds : bond 0.04557 / 3.14 ( 417) hydrogen bonds : angle 4.18370 / 2.99 ( 1133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 74 time to evaluate : 0.223 Fit side-chains REVERT: A 65 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: A 69 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8094 (ttpt) REVERT: A 292 LYS cc_start: 0.6689 (mmtp) cc_final: 0.6193 (mptt) REVERT: A 549 LYS cc_start: 0.2414 (OUTLIER) cc_final: 0.1729 (mppt) REVERT: A 619 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: A 648 LYS cc_start: 0.7619 (mtpt) cc_final: 0.7344 (mtmm) REVERT: A 673 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7836 (tp) REVERT: A 729 ASP cc_start: 0.8039 (m-30) cc_final: 0.7764 (m-30) REVERT: A 768 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7904 (ttpp) REVERT: A 844 LYS cc_start: 0.4836 (OUTLIER) cc_final: 0.4486 (pmtt) REVERT: A 848 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7309 (ttp80) outliers start: 61 outliers final: 34 residues processed: 123 average time/residue: 0.4519 time to fit residues: 60.4592 Evaluate side-chains 112 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 70 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 848 ARG Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 868 LEU Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 370 ASN A 419 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.191813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.156426 restraints weight = 10186.709| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.59 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10429 Z= 0.126 Angle : 0.549 11.658 14705 Z= 0.301 Chirality : 0.040 0.298 1706 Planarity : 0.003 0.028 1364 Dihedral : 23.423 179.920 2930 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.64 % Allowed : 33.42 % Favored : 58.94 % 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: 0.91 (0.28), residues: 841 helix: 1.53 (0.26), residues: 376 sheet: -0.10 (0.65), residues: 69 loop : -0.09 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.016 0.001 TYR A 358 PHE 0.015 0.001 PHE A 758 TRP 0.007 0.001 TRP A 229 HIS 0.006 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (10429) covalent geometry : angle 0.54904 / 0.30 (14705) hydrogen bonds : bond 0.04255 / 2.92 ( 417) hydrogen bonds : angle 4.09180 / 2.92 ( 1133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 74 time to evaluate : 0.411 Fit side-chains REVERT: A 69 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (ttpt) REVERT: A 292 LYS cc_start: 0.6776 (mmtp) cc_final: 0.6318 (mptt) REVERT: A 346 GLU cc_start: 0.6944 (tp30) cc_final: 0.6699 (tp30) REVERT: A 505 LYS cc_start: 0.7461 (mptt) cc_final: 0.7065 (mmmt) REVERT: A 524 LYS cc_start: 0.5399 (OUTLIER) cc_final: 0.4971 (mtmt) REVERT: A 549 LYS cc_start: 0.2342 (OUTLIER) cc_final: 0.1677 (mppt) REVERT: A 619 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6882 (m-30) REVERT: A 648 LYS cc_start: 0.7634 (mtpt) cc_final: 0.7364 (mtmm) REVERT: A 729 ASP cc_start: 0.7970 (m-30) cc_final: 0.7707 (m-30) REVERT: A 768 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7962 (ttpp) REVERT: A 844 LYS cc_start: 0.4870 (OUTLIER) cc_final: 0.4503 (pmtt) REVERT: A 875 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7553 (mmmm) outliers start: 59 outliers final: 33 residues processed: 122 average time/residue: 0.4663 time to fit residues: 62.2289 Evaluate side-chains 113 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 524 LYS Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.191043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164225 restraints weight = 10142.589| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.23 r_work: 0.3236 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10429 Z= 0.139 Angle : 0.558 11.194 14705 Z= 0.305 Chirality : 0.040 0.296 1706 Planarity : 0.004 0.036 1364 Dihedral : 23.314 179.982 2924 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 6.87 % Allowed : 34.33 % Favored : 58.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.29), residues: 841 helix: 1.51 (0.26), residues: 376 sheet: -0.04 (0.65), residues: 69 loop : -0.07 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.016 0.001 TYR A 358 PHE 0.016 0.001 PHE A 747 TRP 0.007 0.001 TRP A 229 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (10429) covalent geometry : angle 0.55754 / 0.30 (14705) hydrogen bonds : bond 0.04310 / 2.96 ( 417) hydrogen bonds : angle 4.06894 / 2.90 ( 1133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 75 time to evaluate : 0.351 Fit side-chains REVERT: A 69 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8405 (ttpt) REVERT: A 161 ASP cc_start: 0.7651 (t0) cc_final: 0.7402 (t0) REVERT: A 346 GLU cc_start: 0.7525 (tp30) cc_final: 0.7192 (tp30) REVERT: A 549 LYS cc_start: 0.2693 (OUTLIER) cc_final: 0.1839 (mppt) REVERT: A 619 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7333 (m-30) REVERT: A 648 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7349 (mtmm) REVERT: A 729 ASP cc_start: 0.8373 (m-30) cc_final: 0.7996 (m-30) REVERT: A 768 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8158 (ttpp) REVERT: A 844 LYS cc_start: 0.4770 (OUTLIER) cc_final: 0.4536 (pmtt) REVERT: A 875 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7782 (mmmm) outliers start: 53 outliers final: 32 residues processed: 117 average time/residue: 0.4593 time to fit residues: 59.0128 Evaluate side-chains 109 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 264 ASN A 370 ASN A 543 ASN A 801 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.185219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.149785 restraints weight = 10077.126| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.62 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10429 Z= 0.256 Angle : 0.691 10.629 14705 Z= 0.368 Chirality : 0.047 0.287 1706 Planarity : 0.005 0.079 1364 Dihedral : 23.488 179.801 2924 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 7.38 % Allowed : 33.94 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.28), residues: 841 helix: 1.13 (0.26), residues: 376 sheet: -0.09 (0.62), residues: 70 loop : -0.21 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 116 TYR 0.019 0.002 TYR A 201 PHE 0.023 0.002 PHE A 758 TRP 0.011 0.002 TRP A 229 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.26 (10429) covalent geometry : angle 0.69095 / 0.37 (14705) hydrogen bonds : bond 0.05455 / 3.79 ( 417) hydrogen bonds : angle 4.31232 / 3.10 ( 1133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 78 time to evaluate : 0.319 Fit side-chains REVERT: A 65 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: A 346 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: A 619 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: A 729 ASP cc_start: 0.8152 (m-30) cc_final: 0.7842 (m-30) REVERT: A 758 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.8052 (p90) REVERT: A 768 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7978 (ttpp) REVERT: A 844 LYS cc_start: 0.4917 (OUTLIER) cc_final: 0.4605 (pmtt) outliers start: 57 outliers final: 32 residues processed: 127 average time/residue: 0.4734 time to fit residues: 65.6232 Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 653 ILE Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 803 ASP Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 23 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 264 ASN A 370 ASN A 419 ASN A 801 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.188015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.160690 restraints weight = 10066.316| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.23 r_work: 0.3184 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10429 Z= 0.171 Angle : 0.610 10.549 14705 Z= 0.332 Chirality : 0.042 0.288 1706 Planarity : 0.004 0.034 1364 Dihedral : 23.443 179.904 2922 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.70 % Allowed : 35.62 % Favored : 58.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.28), residues: 841 helix: 1.22 (0.27), residues: 376 sheet: -0.04 (0.63), residues: 70 loop : -0.21 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 734 TYR 0.018 0.002 TYR A 358 PHE 0.019 0.002 PHE A 758 TRP 0.010 0.001 TRP A 229 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (10429) covalent geometry : angle 0.60997 / 0.33 (14705) hydrogen bonds : bond 0.04675 / 3.24 ( 417) hydrogen bonds : angle 4.24573 / 3.07 ( 1133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 72 time to evaluate : 0.321 Fit side-chains REVERT: A 65 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (mm-40) REVERT: A 137 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7758 (tp40) REVERT: A 346 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7231 (tp30) REVERT: A 505 LYS cc_start: 0.7922 (mptt) cc_final: 0.7027 (mmtp) REVERT: A 549 LYS cc_start: 0.2706 (OUTLIER) cc_final: 0.1763 (mppt) REVERT: A 619 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7409 (m-30) REVERT: A 648 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7435 (mtmm) REVERT: A 729 ASP cc_start: 0.8475 (m-30) cc_final: 0.8098 (m-30) REVERT: A 758 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.8050 (p90) REVERT: A 768 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8156 (ttpp) REVERT: A 844 LYS cc_start: 0.4684 (OUTLIER) cc_final: 0.4458 (pmtt) outliers start: 44 outliers final: 28 residues processed: 109 average time/residue: 0.4865 time to fit residues: 57.9570 Evaluate side-chains 106 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 137 GLN Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 476 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 549 LYS Chi-restraints excluded: chain A residue 619 ASP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 758 PHE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 768 LYS Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 824 ARG Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 879 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.188146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.160792 restraints weight = 10104.096| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.23 r_work: 0.3187 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 10429 Z= 0.228 Angle : 0.894 59.164 14705 Z= 0.522 Chirality : 0.042 0.288 1706 Planarity : 0.004 0.034 1364 Dihedral : 23.442 179.905 2922 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.83 % Allowed : 35.49 % Favored : 58.68 % Cbeta Deviations : 0.12 % 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: 0.62 (0.28), residues: 841 helix: 1.22 (0.27), residues: 376 sheet: -0.04 (0.63), residues: 70 loop : -0.21 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 734 TYR 0.018 0.002 TYR A 358 PHE 0.019 0.002 PHE A 758 TRP 0.010 0.001 TRP A 229 HIS 0.005 0.001 HIS A 533 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (10429) covalent geometry : angle 0.89418 / 0.52 (14705) hydrogen bonds : bond 0.04673 / 3.24 ( 417) hydrogen bonds : angle 4.25356 / 3.07 ( 1133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.30 seconds wall clock time: 40 minutes 27.80 seconds (2427.80 seconds total)