Starting phenix.real_space_refine on Wed Mar 4 07:39:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.map" model { file = "/net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vwj_21418/03_2026/6vwj_21418.cif" } resolution = 4.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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 S 42 5.16 5 C 3802 2.51 5 N 1044 2.21 5 O 1122 1.98 5 H 5789 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11799 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 3865 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 20, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7934 Classifications: {'peptide': 507} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 471} Chain breaks: 4 Time building chain proxies: 2.18, per 1000 atoms: 0.18 Number of scatterers: 11799 At special positions: 0 Unit cell: (92.22, 113.42, 103.88, 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 42 16.00 O 1122 8.00 N 1044 7.00 C 3802 6.00 H 5789 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 633 " - pdb=" SG CYS A 849 " distance=2.03 Simple disulfide: pdb=" SG CYS A 776 " - pdb=" SG CYS A 785 " distance=2.03 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 22 " distance=2.04 Simple disulfide: pdb=" SG CYS B 120 " - pdb=" SG CYS B 148 " distance=2.02 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 181 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 234 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS B 291 " distance=2.02 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 633 " - pdb=" SG CYS B 849 " distance=2.03 Simple disulfide: pdb=" SG CYS B 776 " - pdb=" SG CYS B 785 " distance=2.04 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: 0.84 Conformation dependent library (CDL) restraints added in 392.6 milliseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 18 sheets defined 12.0% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 624 through 629 Processing helix chain 'A' and resid 686 through 700 removed outlier: 4.725A pdb=" N PHE A 692 " --> pdb=" O TYR A 688 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 695 " --> pdb=" O VAL A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 784 Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'B' and resid 15 through 22 removed outlier: 4.349A pdb=" N ASN B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.749A pdb=" N ILE B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 144 through 149 Processing helix chain 'B' and resid 249 through 253 Processing helix chain 'B' and resid 625 through 630 removed outlier: 4.346A pdb=" N ARG B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 630' Processing helix chain 'B' and resid 779 through 784 Processing helix chain 'B' and resid 852 through 859 Processing sheet with id=AA1, first strand: chain 'A' and resid 585 through 593 removed outlier: 4.999A pdb=" N ASP A 586 " --> pdb=" O ASN A 602 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN A 602 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN A 592 " --> pdb=" O GLN A 596 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLN A 596 " --> pdb=" O ASN A 592 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 747 through 752 removed outlier: 3.800A pdb=" N TYR A 614 " --> pdb=" O VAL A 752 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 809 through 813 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 875 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TRP A 886 " --> pdb=" O ILE A 875 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA A 877 " --> pdb=" O GLY A 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 846 through 851 removed outlier: 3.745A pdb=" N MET A 834 " --> pdb=" O THR A 878 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.691A pdb=" N ILE B 76 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 7 through 10 removed outlier: 6.840A pdb=" N LEU B 29 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N PHE B 58 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 31 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N TYR B 85 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ARG B 112 " --> pdb=" O TYR B 85 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 87 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N GLU B 114 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 89 " --> pdb=" O GLU B 114 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AA9, first strand: chain 'B' and resid 175 through 177 Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 209 removed outlier: 4.097A pdb=" N ALA B 220 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N SER B 208 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N CYS B 218 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AB3, first strand: chain 'B' and resid 245 through 248 removed outlier: 8.084A pdb=" N CYS B 273 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG B 240 " --> pdb=" O CYS B 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 281 through 283 Processing sheet with id=AB5, first strand: chain 'B' and resid 585 through 590 removed outlier: 5.145A pdb=" N ASP B 586 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASN B 602 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 747 through 751 Processing sheet with id=AB7, first strand: chain 'B' and resid 809 through 813 Processing sheet with id=AB8, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 846 through 851 removed outlier: 3.700A pdb=" N MET B 834 " --> pdb=" O THR B 878 " (cutoff:3.500A) 209 hydrogen bonds defined for protein. 528 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: 2.55 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5789 1.03 - 1.23: 471 1.23 - 1.44: 2236 1.44 - 1.64: 3410 1.64 - 1.84: 50 Bond restraints: 11956 Sorted by residual: bond pdb=" N VAL A 580 " pdb=" CA VAL A 580 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.77e+00 bond pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " ideal model delta sigma weight residual 1.808 1.758 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" N VAL A 580 " pdb=" H VAL A 580 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.13e+00 bond pdb=" CB LYS A 897 " pdb=" CG LYS A 897 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB CYS A 785 " pdb=" SG CYS A 785 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.57e+00 ... (remaining 11951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 20600 1.70 - 3.40: 842 3.40 - 5.10: 89 5.10 - 6.80: 21 6.80 - 8.50: 1 Bond angle restraints: 21553 Sorted by residual: angle pdb=" N ASN B 11 " pdb=" CA ASN B 11 " pdb=" C ASN B 11 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 angle pdb=" CA LYS B 600 " pdb=" CB LYS B 600 " pdb=" CG LYS B 600 " ideal model delta sigma weight residual 114.10 107.58 6.52 2.00e+00 2.50e-01 1.06e+01 angle pdb=" N ASP B 12 " pdb=" CA ASP B 12 " pdb=" C ASP B 12 " ideal model delta sigma weight residual 109.06 114.51 -5.45 1.70e+00 3.46e-01 1.03e+01 angle pdb=" CA TYR A 628 " pdb=" CB TYR A 628 " pdb=" CG TYR A 628 " ideal model delta sigma weight residual 113.90 119.60 -5.70 1.80e+00 3.09e-01 1.00e+01 angle pdb=" CA LYS A 862 " pdb=" CB LYS A 862 " pdb=" CG LYS A 862 " ideal model delta sigma weight residual 114.10 107.84 6.26 2.00e+00 2.50e-01 9.80e+00 ... (remaining 21548 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5204 17.48 - 34.96: 344 34.96 - 52.45: 111 52.45 - 69.93: 84 69.93 - 87.41: 7 Dihedral angle restraints: 5750 sinusoidal: 3133 harmonic: 2617 Sorted by residual: dihedral pdb=" CB CYS B 205 " pdb=" SG CYS B 205 " pdb=" SG CYS B 218 " pdb=" CB CYS B 218 " ideal model delta sinusoidal sigma weight residual -86.00 -145.73 59.73 1 1.00e+01 1.00e-02 4.76e+01 dihedral pdb=" CA SER B 788 " pdb=" C SER B 788 " pdb=" N ASN B 789 " pdb=" CA ASN B 789 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA SER A 788 " pdb=" C SER A 788 " pdb=" N ASN A 789 " pdb=" CA ASN A 789 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 456 0.035 - 0.070: 245 0.070 - 0.105: 110 0.105 - 0.140: 52 0.140 - 0.175: 11 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA ASN B 11 " pdb=" N ASN B 11 " pdb=" C ASN B 11 " pdb=" CB ASN B 11 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE A 832 " pdb=" N ILE A 832 " pdb=" C ILE A 832 " pdb=" CB ILE A 832 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 871 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 112 " -0.099 9.50e-02 1.11e+02 4.89e-02 3.05e+01 pdb=" NE ARG B 112 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG B 112 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG B 112 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG B 112 " 0.039 2.00e-02 2.50e+03 pdb="HH11 ARG B 112 " -0.016 2.00e-02 2.50e+03 pdb="HH12 ARG B 112 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B 112 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 112 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 865 " 0.032 9.50e-02 1.11e+02 3.24e-02 2.12e+01 pdb=" NE ARG A 865 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 865 " 0.038 2.00e-02 2.50e+03 pdb=" NH1 ARG A 865 " -0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 865 " 0.041 2.00e-02 2.50e+03 pdb="HH11 ARG A 865 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 865 " 0.027 2.00e-02 2.50e+03 pdb="HH21 ARG A 865 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 865 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 269 " -0.001 2.00e-02 2.50e+03 2.84e-02 1.81e+01 pdb=" CG HIS B 269 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS B 269 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 269 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS B 269 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 HIS B 269 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS B 269 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 HIS B 269 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS B 269 " 0.041 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 335 2.09 - 2.72: 20056 2.72 - 3.35: 33407 3.35 - 3.97: 41862 3.97 - 4.60: 65099 Nonbonded interactions: 160759 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 635 " pdb=" OE2 GLU B 836 " model vdw 1.463 2.450 nonbonded pdb=" HH TYR B 171 " pdb=" O LEU B 880 " model vdw 1.471 2.450 nonbonded pdb="HH11 ARG B 874 " pdb=" O THR B 887 " model vdw 1.484 2.450 nonbonded pdb=" O ASN A 610 " pdb=" H HIS A 778 " model vdw 1.507 2.450 nonbonded pdb=" OD2 ASP A 586 " pdb="HD21 ASN A 602 " model vdw 1.527 2.450 ... (remaining 160754 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: 4.890 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: 0.070 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.980 Find NCS groups from input model: 0.030 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 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 0.050 6184 Z= 0.223 Angle : 0.996 8.496 8404 Z= 0.564 Chirality : 0.055 0.175 874 Planarity : 0.006 0.060 1101 Dihedral : 13.450 80.669 2316 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.79 % Favored : 94.80 % Rotamer: Outliers : 1.20 % Allowed : 4.19 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.29), residues: 731 helix: -3.55 (0.43), residues: 65 sheet: 0.23 (0.36), residues: 212 loop : -0.87 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.089 0.009 ARG B 112 TYR 0.025 0.006 TYR A 628 PHE 0.020 0.003 PHE B 90 TRP 0.021 0.004 TRP B 176 HIS 0.017 0.003 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00509 ( 6167) covalent geometry : angle 0.98936 ( 8370) SS BOND : bond 0.00421 ( 17) SS BOND : angle 2.04624 ( 34) hydrogen bonds : bond 0.27436 ( 183) hydrogen bonds : angle 10.13624 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 870 ASN cc_start: 0.4986 (m-40) cc_final: 0.4719 (m-40) REVERT: B 131 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7257 (pp) REVERT: B 878 THR cc_start: 0.8570 (m) cc_final: 0.8307 (p) outliers start: 8 outliers final: 3 residues processed: 107 average time/residue: 0.1656 time to fit residues: 23.3308 Evaluate side-chains 68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.097164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.083741 restraints weight = 106240.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.085985 restraints weight = 57726.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.087554 restraints weight = 38215.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.088545 restraints weight = 28822.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.089164 restraints weight = 23999.964| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6184 Z= 0.168 Angle : 0.706 6.201 8404 Z= 0.383 Chirality : 0.048 0.163 874 Planarity : 0.005 0.045 1101 Dihedral : 6.853 29.739 831 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.65 % Favored : 95.08 % Rotamer: Outliers : 0.15 % Allowed : 3.14 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % 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: -0.79 (0.30), residues: 731 helix: -2.12 (0.57), residues: 54 sheet: -0.22 (0.35), residues: 201 loop : -0.42 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 874 TYR 0.016 0.002 TYR A 858 PHE 0.017 0.002 PHE B 45 TRP 0.009 0.001 TRP B 618 HIS 0.007 0.002 HIS B 778 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6167) covalent geometry : angle 0.69827 ( 8370) SS BOND : bond 0.00541 ( 17) SS BOND : angle 1.79782 ( 34) hydrogen bonds : bond 0.04695 ( 183) hydrogen bonds : angle 7.70960 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 ASN cc_start: 0.8938 (m-40) cc_final: 0.8622 (m-40) REVERT: B 852 ARG cc_start: 0.6467 (ttt-90) cc_final: 0.6133 (ptm160) outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1548 time to fit residues: 15.3632 Evaluate side-chains 53 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 26 optimal weight: 0.0170 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 62 optimal weight: 0.5980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.096852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.083093 restraints weight = 105480.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.085555 restraints weight = 57356.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.087092 restraints weight = 37600.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.088119 restraints weight = 28344.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.088570 restraints weight = 23409.442| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6184 Z= 0.131 Angle : 0.624 5.903 8404 Z= 0.335 Chirality : 0.047 0.155 874 Planarity : 0.005 0.042 1101 Dihedral : 6.286 31.215 831 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.85 (0.30), residues: 731 helix: -2.02 (0.59), residues: 63 sheet: -0.48 (0.34), residues: 213 loop : -0.30 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 617 TYR 0.013 0.001 TYR B 239 PHE 0.013 0.001 PHE A 892 TRP 0.009 0.001 TRP B 618 HIS 0.005 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6167) covalent geometry : angle 0.61682 ( 8370) SS BOND : bond 0.00524 ( 17) SS BOND : angle 1.55938 ( 34) hydrogen bonds : bond 0.03872 ( 183) hydrogen bonds : angle 7.00717 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6758 (tm-30) REVERT: B 602 ASN cc_start: 0.8878 (t0) cc_final: 0.8406 (t0) REVERT: B 810 TRP cc_start: 0.5433 (p-90) cc_final: 0.5191 (p-90) REVERT: B 833 LEU cc_start: 0.8973 (mm) cc_final: 0.8264 (tp) REVERT: B 834 MET cc_start: 0.6702 (ptm) cc_final: 0.6437 (ptp) REVERT: B 852 ARG cc_start: 0.6347 (ttt-90) cc_final: 0.6068 (ptm160) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1492 time to fit residues: 13.5739 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 ASN B 269 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.096404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.082822 restraints weight = 107443.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.085021 restraints weight = 58852.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.086578 restraints weight = 39104.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.087577 restraints weight = 29537.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.088038 restraints weight = 24414.035| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6184 Z= 0.131 Angle : 0.598 6.251 8404 Z= 0.322 Chirality : 0.046 0.150 874 Planarity : 0.004 0.042 1101 Dihedral : 5.943 30.729 831 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.79 % Favored : 95.08 % Rotamer: Outliers : 0.15 % Allowed : 0.75 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.85 (0.30), residues: 731 helix: -1.79 (0.64), residues: 57 sheet: -0.59 (0.34), residues: 217 loop : -0.29 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 174 TYR 0.014 0.001 TYR B 13 PHE 0.011 0.001 PHE B 281 TRP 0.009 0.001 TRP B 618 HIS 0.005 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6167) covalent geometry : angle 0.59104 ( 8370) SS BOND : bond 0.00235 ( 17) SS BOND : angle 1.56170 ( 34) hydrogen bonds : bond 0.03468 ( 183) hydrogen bonds : angle 6.78204 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.8084 (m-30) cc_final: 0.7736 (t0) REVERT: A 693 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6917 (tm-30) REVERT: B 602 ASN cc_start: 0.8891 (t0) cc_final: 0.8423 (t0) REVERT: B 810 TRP cc_start: 0.5281 (p-90) cc_final: 0.5041 (p-90) REVERT: B 833 LEU cc_start: 0.9016 (mm) cc_final: 0.8291 (tp) REVERT: B 852 ARG cc_start: 0.6325 (ttt-90) cc_final: 0.5977 (ptm160) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1569 time to fit residues: 14.6292 Evaluate side-chains 52 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.096472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.083230 restraints weight = 105522.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.085413 restraints weight = 57059.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.086970 restraints weight = 37556.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.087957 restraints weight = 28181.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.088519 restraints weight = 23234.551| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6184 Z= 0.109 Angle : 0.559 6.435 8404 Z= 0.300 Chirality : 0.046 0.147 874 Planarity : 0.004 0.042 1101 Dihedral : 5.599 32.735 831 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.83 (0.30), residues: 731 helix: -1.60 (0.65), residues: 57 sheet: -0.66 (0.34), residues: 217 loop : -0.26 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 874 TYR 0.013 0.001 TYR A 628 PHE 0.009 0.001 PHE A 892 TRP 0.010 0.001 TRP B 618 HIS 0.008 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6167) covalent geometry : angle 0.55563 ( 8370) SS BOND : bond 0.00336 ( 17) SS BOND : angle 1.12770 ( 34) hydrogen bonds : bond 0.03228 ( 183) hydrogen bonds : angle 6.41087 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.7988 (m-30) cc_final: 0.7636 (t0) REVERT: A 693 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6949 (tm-30) REVERT: B 602 ASN cc_start: 0.8939 (t0) cc_final: 0.8576 (t0) REVERT: B 833 LEU cc_start: 0.9015 (mm) cc_final: 0.8334 (tp) REVERT: B 834 MET cc_start: 0.6658 (ptm) cc_final: 0.6358 (ptp) REVERT: B 852 ARG cc_start: 0.6264 (ttt-90) cc_final: 0.5954 (ptm160) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1502 time to fit residues: 13.7171 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.0270 chunk 58 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 608 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.096710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.083302 restraints weight = 106053.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.085451 restraints weight = 57548.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.086927 restraints weight = 38114.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.087953 restraints weight = 28810.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.088442 restraints weight = 23815.429| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6184 Z= 0.106 Angle : 0.561 6.671 8404 Z= 0.301 Chirality : 0.046 0.145 874 Planarity : 0.004 0.042 1101 Dihedral : 5.481 31.919 831 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.47 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.82 (0.31), residues: 731 helix: -1.48 (0.63), residues: 63 sheet: -0.71 (0.34), residues: 217 loop : -0.21 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 847 TYR 0.016 0.001 TYR B 13 PHE 0.009 0.001 PHE A 892 TRP 0.014 0.001 TRP B 244 HIS 0.008 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6167) covalent geometry : angle 0.55546 ( 8370) SS BOND : bond 0.00176 ( 17) SS BOND : angle 1.32370 ( 34) hydrogen bonds : bond 0.03238 ( 183) hydrogen bonds : angle 6.18536 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 693 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6950 (tm-30) REVERT: B 602 ASN cc_start: 0.8860 (t0) cc_final: 0.8500 (t0) REVERT: B 833 LEU cc_start: 0.9025 (mm) cc_final: 0.8364 (tp) REVERT: B 834 MET cc_start: 0.6632 (ptm) cc_final: 0.6303 (ptp) REVERT: B 852 ARG cc_start: 0.6251 (ttt-90) cc_final: 0.5947 (ptm160) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.1408 time to fit residues: 12.6944 Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 6 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.096173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.082946 restraints weight = 103638.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.085088 restraints weight = 56457.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.086622 restraints weight = 37155.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.087644 restraints weight = 27842.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.088185 restraints weight = 22902.559| |-----------------------------------------------------------------------------| r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6184 Z= 0.115 Angle : 0.561 6.994 8404 Z= 0.300 Chirality : 0.046 0.143 874 Planarity : 0.004 0.042 1101 Dihedral : 5.400 31.247 831 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.16 % Favored : 93.71 % Rotamer: Outliers : 0.15 % Allowed : 0.60 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -0.80 (0.31), residues: 731 helix: -1.36 (0.67), residues: 63 sheet: -0.72 (0.34), residues: 217 loop : -0.20 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 874 TYR 0.013 0.001 TYR B 13 PHE 0.010 0.001 PHE A 892 TRP 0.019 0.001 TRP B 886 HIS 0.008 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6167) covalent geometry : angle 0.55615 ( 8370) SS BOND : bond 0.00200 ( 17) SS BOND : angle 1.32838 ( 34) hydrogen bonds : bond 0.03134 ( 183) hydrogen bonds : angle 6.14088 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 624 ASP cc_start: 0.8166 (m-30) cc_final: 0.7709 (t0) REVERT: A 693 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7001 (tm-30) REVERT: B 602 ASN cc_start: 0.8899 (t0) cc_final: 0.8562 (t0) REVERT: B 833 LEU cc_start: 0.9013 (mm) cc_final: 0.8393 (tp) REVERT: B 834 MET cc_start: 0.6564 (ptm) cc_final: 0.6283 (ptp) REVERT: B 852 ARG cc_start: 0.6279 (ttt-90) cc_final: 0.6019 (ptm160) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.1451 time to fit residues: 13.6212 Evaluate side-chains 55 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 876 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.095312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.082098 restraints weight = 103736.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.084279 restraints weight = 56041.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.085745 restraints weight = 36866.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.086761 restraints weight = 27841.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.087297 restraints weight = 22849.152| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6701 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6184 Z= 0.143 Angle : 0.578 7.178 8404 Z= 0.309 Chirality : 0.046 0.144 874 Planarity : 0.005 0.042 1101 Dihedral : 5.479 29.974 831 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.98 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.31), residues: 731 helix: -1.92 (0.62), residues: 63 sheet: -0.81 (0.33), residues: 222 loop : -0.37 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 10 TYR 0.009 0.001 TYR B 239 PHE 0.014 0.001 PHE A 695 TRP 0.009 0.001 TRP B 618 HIS 0.008 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6167) covalent geometry : angle 0.57347 ( 8370) SS BOND : bond 0.00285 ( 17) SS BOND : angle 1.21827 ( 34) hydrogen bonds : bond 0.03262 ( 183) hydrogen bonds : angle 6.23364 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8921 (t0) cc_final: 0.8596 (t0) REVERT: B 833 LEU cc_start: 0.9050 (mm) cc_final: 0.8461 (tp) REVERT: B 852 ARG cc_start: 0.6303 (ttt180) cc_final: 0.6062 (ptm160) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1519 time to fit residues: 13.2268 Evaluate side-chains 54 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.093198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.079699 restraints weight = 104442.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.082049 restraints weight = 57047.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.083539 restraints weight = 37725.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.084516 restraints weight = 28375.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.084899 restraints weight = 23453.056| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 6184 Z= 0.189 Angle : 0.643 7.283 8404 Z= 0.347 Chirality : 0.047 0.151 874 Planarity : 0.005 0.043 1101 Dihedral : 5.890 29.245 831 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.76 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.31), residues: 731 helix: -1.77 (0.70), residues: 53 sheet: -1.18 (0.34), residues: 210 loop : -0.54 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 874 TYR 0.015 0.002 TYR B 13 PHE 0.017 0.002 PHE A 695 TRP 0.010 0.002 TRP B 618 HIS 0.009 0.002 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 6167) covalent geometry : angle 0.63849 ( 8370) SS BOND : bond 0.00377 ( 17) SS BOND : angle 1.33773 ( 34) hydrogen bonds : bond 0.03616 ( 183) hydrogen bonds : angle 6.71540 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8964 (t0) cc_final: 0.8697 (t0) REVERT: B 833 LEU cc_start: 0.9066 (mm) cc_final: 0.8560 (tp) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1596 time to fit residues: 12.6141 Evaluate side-chains 46 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.095571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.082020 restraints weight = 102042.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.084165 restraints weight = 55235.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.085702 restraints weight = 36494.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.086719 restraints weight = 27338.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.087350 restraints weight = 22421.283| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6184 Z= 0.119 Angle : 0.578 7.191 8404 Z= 0.310 Chirality : 0.047 0.143 874 Planarity : 0.006 0.095 1101 Dihedral : 5.618 25.965 831 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.80 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.31), residues: 731 helix: -1.48 (0.72), residues: 53 sheet: -0.95 (0.34), residues: 216 loop : -0.51 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 852 TYR 0.013 0.001 TYR B 13 PHE 0.014 0.001 PHE A 695 TRP 0.009 0.001 TRP B 886 HIS 0.009 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 6167) covalent geometry : angle 0.57349 ( 8370) SS BOND : bond 0.00207 ( 17) SS BOND : angle 1.24076 ( 34) hydrogen bonds : bond 0.03189 ( 183) hydrogen bonds : angle 6.33785 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 602 ASN cc_start: 0.8952 (t0) cc_final: 0.8699 (t0) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1531 time to fit residues: 12.9005 Evaluate side-chains 49 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.095101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.081573 restraints weight = 102383.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.083701 restraints weight = 55747.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.085226 restraints weight = 36872.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.086237 restraints weight = 27677.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.086833 restraints weight = 22763.613| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.6202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6184 Z= 0.135 Angle : 0.579 7.347 8404 Z= 0.310 Chirality : 0.046 0.144 874 Planarity : 0.005 0.045 1101 Dihedral : 5.523 24.390 831 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.89 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.31), residues: 731 helix: -1.45 (0.72), residues: 53 sheet: -0.94 (0.33), residues: 225 loop : -0.51 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 852 TYR 0.016 0.001 TYR B 13 PHE 0.012 0.001 PHE A 695 TRP 0.008 0.001 TRP B 886 HIS 0.010 0.001 HIS A 774 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 6167) covalent geometry : angle 0.57481 ( 8370) SS BOND : bond 0.00225 ( 17) SS BOND : angle 1.24881 ( 34) hydrogen bonds : bond 0.03210 ( 183) hydrogen bonds : angle 6.35229 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2536.59 seconds wall clock time: 43 minutes 44.57 seconds (2624.57 seconds total)