Starting phenix.real_space_refine on Tue Feb 3 12:38:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.map" model { file = "/net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xbp_66708/02_2026/9xbp_66708.cif" } resolution = 2.2 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 ------------------------------------------------------------------------------- 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= 0.005 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1370 2.51 5 N 415 2.21 5 O 485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2275 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 450 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.50, per 1000 atoms: 0.22 Number of scatterers: 2275 At special positions: 0 Unit cell: (61.42, 61.42, 44.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 485 8.00 N 415 7.00 C 1370 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: 0.17 Conformation dependent library (CDL) restraints added in 86.0 milliseconds 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 490 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 55.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 88 through 89 removed outlier: 6.934A pdb=" N TYR A 88 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR C 88 " --> pdb=" O GLN E 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 98 through 110 removed outlier: 6.767A pdb=" N ARG B 98 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N TYR D 101 " --> pdb=" O ARG B 98 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ASN B 100 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN D 103 " --> pdb=" O ASN B 100 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N LYS B 102 " --> pdb=" O ASN D 103 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN D 105 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N PHE B 104 " --> pdb=" O ASN D 105 " (cutoff:3.500A) removed outlier: 10.172A pdb=" N ASN D 107 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N TYR B 106 " --> pdb=" O ASN D 107 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N ASN D 109 " --> pdb=" O TYR B 106 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASN B 108 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A 98 " --> pdb=" O GLY B 99 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR B 101 " --> pdb=" O ARG A 98 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN A 100 " --> pdb=" O TYR B 101 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN B 103 " --> pdb=" O ASN A 100 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N LYS A 102 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N ASN B 105 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N PHE A 104 " --> pdb=" O ASN B 105 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N ASN B 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 9.203A pdb=" N TYR A 106 " --> pdb=" O ASN B 107 " (cutoff:3.500A) removed outlier: 9.945A pdb=" N ASN B 109 " --> pdb=" O TYR A 106 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N ASN A 108 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE C 104 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASN A 105 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N TYR C 106 " --> pdb=" O ASN A 105 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ASN A 107 " --> pdb=" O TYR C 106 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASN C 108 " --> pdb=" O ASN A 107 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ASN A 109 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU C 110 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE E 104 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN C 105 " --> pdb=" O PHE E 104 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR E 106 " --> pdb=" O ASN C 105 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASN C 107 " --> pdb=" O TYR E 106 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN E 108 " --> pdb=" O ASN C 107 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN C 109 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU E 110 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 113 through 117 removed outlier: 6.965A pdb=" N PHE D 117 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N PHE B 117 " --> pdb=" O GLY A 116 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TYR A 113 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY C 116 " --> pdb=" O TYR A 113 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N ALA A 115 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR C 113 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY E 116 " --> pdb=" O TYR C 113 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA C 115 " --> pdb=" O GLY E 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 124 through 128 removed outlier: 6.425A pdb=" N MET B 124 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASN D 127 " --> pdb=" O MET B 124 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 126 " --> pdb=" O ASN D 127 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N MET A 124 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASN B 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 126 " --> pdb=" O ASN B 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 218 through 228 removed outlier: 6.654A pdb=" N LYS B 219 " --> pdb=" O ILE D 220 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU D 222 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER B 221 " --> pdb=" O GLU D 222 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR D 224 " --> pdb=" O SER B 221 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER B 223 " --> pdb=" O THR D 224 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ASN D 226 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS B 225 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN D 228 " --> pdb=" O HIS B 225 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 227 " --> pdb=" O ASN D 228 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A 219 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLU B 222 " --> pdb=" O LYS A 219 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER A 221 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N THR B 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER A 223 " --> pdb=" O THR B 224 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ASN B 226 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N HIS A 225 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ASN B 228 " --> pdb=" O HIS A 225 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 227 " --> pdb=" O ASN B 228 " (cutoff:3.500A) 46 hydrogen bonds defined for protein. 138 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: 0.29 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 800 1.34 - 1.46: 473 1.46 - 1.57: 1012 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 2295 Sorted by residual: bond pdb=" C ASN E 228 " pdb=" N ASN E 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.40e-02 5.10e+03 4.14e+00 bond pdb=" C ASN D 228 " pdb=" N ASN D 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.40e-02 5.10e+03 3.96e+00 bond pdb=" C ASN B 228 " pdb=" N ASN B 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.40e-02 5.10e+03 3.95e+00 bond pdb=" C ASN A 228 " pdb=" N ASN A 229 " ideal model delta sigma weight residual 1.329 1.357 -0.028 1.40e-02 5.10e+03 3.88e+00 bond pdb=" C ASN C 228 " pdb=" N ASN C 229 " ideal model delta sigma weight residual 1.329 1.356 -0.027 1.40e-02 5.10e+03 3.85e+00 ... (remaining 2290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.83: 2800 0.83 - 1.66: 230 1.66 - 2.50: 40 2.50 - 3.33: 5 3.33 - 4.16: 5 Bond angle restraints: 3080 Sorted by residual: angle pdb=" N GLN D 120 " pdb=" CA GLN D 120 " pdb=" CB GLN D 120 " ideal model delta sigma weight residual 112.30 110.32 1.98 1.52e+00 4.33e-01 1.70e+00 angle pdb=" N GLN E 120 " pdb=" CA GLN E 120 " pdb=" CB GLN E 120 " ideal model delta sigma weight residual 112.30 110.32 1.98 1.52e+00 4.33e-01 1.69e+00 angle pdb=" N GLN B 120 " pdb=" CA GLN B 120 " pdb=" CB GLN B 120 " ideal model delta sigma weight residual 112.30 110.34 1.96 1.52e+00 4.33e-01 1.66e+00 angle pdb=" N GLN A 120 " pdb=" CA GLN A 120 " pdb=" CB GLN A 120 " ideal model delta sigma weight residual 112.30 110.34 1.96 1.52e+00 4.33e-01 1.65e+00 angle pdb=" N GLN C 120 " pdb=" CA GLN C 120 " pdb=" CB GLN C 120 " ideal model delta sigma weight residual 112.30 110.35 1.95 1.52e+00 4.33e-01 1.65e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.01: 1064 8.01 - 16.03: 151 16.03 - 24.04: 65 24.04 - 32.06: 35 32.06 - 40.07: 15 Dihedral angle restraints: 1330 sinusoidal: 550 harmonic: 780 Sorted by residual: dihedral pdb=" CA ASN E 93 " pdb=" C ASN E 93 " pdb=" N PRO E 94 " pdb=" CA PRO E 94 " ideal model delta harmonic sigma weight residual 180.00 167.56 12.44 0 5.00e+00 4.00e-02 6.19e+00 dihedral pdb=" CA ASN D 93 " pdb=" C ASN D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual 180.00 167.60 12.40 0 5.00e+00 4.00e-02 6.15e+00 dihedral pdb=" CA ASN A 93 " pdb=" C ASN A 93 " pdb=" N PRO A 94 " pdb=" CA PRO A 94 " ideal model delta harmonic sigma weight residual 180.00 167.60 12.40 0 5.00e+00 4.00e-02 6.15e+00 ... (remaining 1327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 141 0.023 - 0.045: 109 0.045 - 0.068: 15 0.068 - 0.090: 5 0.090 - 0.113: 5 Chirality restraints: 275 Sorted by residual: chirality pdb=" CA ILE A 220 " pdb=" N ILE A 220 " pdb=" C ILE A 220 " pdb=" CB ILE A 220 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.17e-01 chirality pdb=" CA ILE B 220 " pdb=" N ILE B 220 " pdb=" C ILE B 220 " pdb=" CB ILE B 220 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.13e-01 chirality pdb=" CA ILE C 220 " pdb=" N ILE C 220 " pdb=" C ILE C 220 " pdb=" CB ILE C 220 " both_signs ideal model delta sigma weight residual False 2.43 2.54 -0.11 2.00e-01 2.50e+01 3.10e-01 ... (remaining 272 not shown) Planarity restraints: 445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 102 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C LYS C 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS C 102 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN C 103 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 102 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C LYS B 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS B 102 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 103 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 102 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C LYS A 102 " -0.036 2.00e-02 2.50e+03 pdb=" O LYS A 102 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 103 " 0.012 2.00e-02 2.50e+03 ... (remaining 442 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 1145 2.96 - 3.44: 1882 3.44 - 3.93: 4275 3.93 - 4.41: 4705 4.41 - 4.90: 7967 Nonbonded interactions: 19974 Sorted by model distance: nonbonded pdb=" OH TYR C 106 " pdb=" O HOH C 301 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR D 106 " pdb=" O HOH D 301 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR B 106 " pdb=" O HOH B 301 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR A 106 " pdb=" O HOH A 301 " model vdw 2.470 3.040 nonbonded pdb=" OH TYR E 106 " pdb=" O HOH E 301 " model vdw 2.471 3.040 ... (remaining 19969 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.590 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.960 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:5.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 0.002 0.028 2295 Z= 0.129 Angle : 0.507 4.162 3080 Z= 0.288 Chirality : 0.031 0.113 275 Planarity : 0.004 0.021 445 Dihedral : 10.967 40.073 840 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -4.49 (0.24), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.19), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 98 TYR 0.006 0.001 TYR E 101 PHE 0.009 0.001 PHE B 92 HIS 0.000 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 2295) covalent geometry : angle 0.50699 ( 3080) hydrogen bonds : bond 0.17000 ( 46) hydrogen bonds : angle 11.32669 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: C 98 ARG cc_start: 0.7371 (ptt90) cc_final: 0.7087 (ptt90) REVERT: E 219 LYS cc_start: 0.7683 (tptp) cc_final: 0.7440 (tttp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.6962 time to fit residues: 24.7232 Evaluate side-chains 29 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.2980 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 105 ASN B 105 ASN C 105 ASN C 111 GLN C 122 GLN D 105 ASN E 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092740 restraints weight = 1533.928| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.27 r_work: 0.3007 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2295 Z= 0.146 Angle : 0.584 4.560 3080 Z= 0.324 Chirality : 0.039 0.128 275 Planarity : 0.003 0.016 445 Dihedral : 4.419 13.624 295 Min Nonbonded Distance : 2.676 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: -3.94 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 98 TYR 0.014 0.002 TYR E 101 PHE 0.014 0.002 PHE A 117 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 2295) covalent geometry : angle 0.58373 ( 3080) hydrogen bonds : bond 0.04828 ( 46) hydrogen bonds : angle 7.36051 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.090 Fit side-chains revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8244 (tptp) cc_final: 0.7929 (tttt) REVERT: C 98 ARG cc_start: 0.7918 (ptt90) cc_final: 0.7607 (ptt90) REVERT: C 219 LYS cc_start: 0.8090 (tttp) cc_final: 0.7376 (mttp) REVERT: D 219 LYS cc_start: 0.8165 (tptp) cc_final: 0.7573 (ttpt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.5832 time to fit residues: 24.9724 Evaluate side-chains 40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 ASN B 228 ASN E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.142253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092888 restraints weight = 1566.288| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.27 r_work: 0.3011 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2295 Z= 0.119 Angle : 0.559 6.898 3080 Z= 0.300 Chirality : 0.037 0.126 275 Planarity : 0.002 0.010 445 Dihedral : 4.355 14.401 295 Min Nonbonded Distance : 2.679 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -3.75 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.18), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 98 TYR 0.011 0.001 TYR E 101 PHE 0.010 0.002 PHE C 92 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2295) covalent geometry : angle 0.55935 ( 3080) hydrogen bonds : bond 0.04152 ( 46) hydrogen bonds : angle 6.40427 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 LYS cc_start: 0.8203 (tptp) cc_final: 0.7986 (tttt) REVERT: C 98 ARG cc_start: 0.7883 (ptt90) cc_final: 0.7588 (ptt-90) REVERT: C 219 LYS cc_start: 0.8077 (tttp) cc_final: 0.7385 (mttp) REVERT: D 228 ASN cc_start: 0.8345 (t0) cc_final: 0.8011 (t0) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5553 time to fit residues: 25.5124 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 228 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091280 restraints weight = 1579.381| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.27 r_work: 0.2980 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2295 Z= 0.186 Angle : 0.631 7.716 3080 Z= 0.341 Chirality : 0.039 0.126 275 Planarity : 0.003 0.015 445 Dihedral : 4.606 15.825 295 Min Nonbonded Distance : 2.686 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.42 % Allowed : 5.83 % Favored : 93.75 % 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: -3.78 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.18), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.011 0.002 TYR E 101 PHE 0.011 0.003 PHE C 92 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2295) covalent geometry : angle 0.63068 ( 3080) hydrogen bonds : bond 0.05093 ( 46) hydrogen bonds : angle 6.19519 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.054 Fit side-chains REVERT: A 219 LYS cc_start: 0.8210 (tptp) cc_final: 0.7981 (tttt) REVERT: B 98 ARG cc_start: 0.8201 (ptt90) cc_final: 0.7914 (ptm-80) REVERT: C 98 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7727 (ptt-90) REVERT: C 219 LYS cc_start: 0.8087 (tttp) cc_final: 0.7411 (mttp) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.5124 time to fit residues: 21.9215 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091903 restraints weight = 1566.892| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.27 r_work: 0.2989 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2295 Z= 0.161 Angle : 0.618 7.851 3080 Z= 0.328 Chirality : 0.038 0.126 275 Planarity : 0.003 0.016 445 Dihedral : 4.507 15.125 295 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.83 % Allowed : 6.67 % Favored : 92.50 % 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: -3.83 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.18), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.010 0.002 TYR E 101 PHE 0.011 0.002 PHE C 92 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2295) covalent geometry : angle 0.61793 ( 3080) hydrogen bonds : bond 0.04679 ( 46) hydrogen bonds : angle 5.99547 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.056 Fit side-chains REVERT: A 219 LYS cc_start: 0.8215 (tptp) cc_final: 0.7982 (tttt) REVERT: B 98 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7890 (ptt-90) REVERT: C 98 ARG cc_start: 0.7965 (ptt90) cc_final: 0.7618 (ptt-90) REVERT: C 219 LYS cc_start: 0.8057 (tttp) cc_final: 0.7404 (mttp) REVERT: E 219 LYS cc_start: 0.8088 (mtpm) cc_final: 0.7824 (mtpt) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.4497 time to fit residues: 19.2413 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 15 optimal weight: 0.0050 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 6 optimal weight: 0.9990 overall best weight: 1.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.143150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093979 restraints weight = 1566.241| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.27 r_work: 0.3029 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2295 Z= 0.089 Angle : 0.542 7.128 3080 Z= 0.281 Chirality : 0.036 0.125 275 Planarity : 0.002 0.010 445 Dihedral : 4.164 13.580 295 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % 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: -3.87 (0.22), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 98 TYR 0.009 0.001 TYR E 101 PHE 0.011 0.001 PHE C 92 HIS 0.001 0.000 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 2295) covalent geometry : angle 0.54214 ( 3080) hydrogen bonds : bond 0.03366 ( 46) hydrogen bonds : angle 5.74477 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.053 Fit side-chains REVERT: B 98 ARG cc_start: 0.8064 (ptt90) cc_final: 0.7721 (ptm-80) REVERT: C 98 ARG cc_start: 0.7839 (ptt90) cc_final: 0.7489 (ptt-90) REVERT: C 219 LYS cc_start: 0.8090 (tttp) cc_final: 0.7441 (mttp) REVERT: D 98 ARG cc_start: 0.7764 (ptt90) cc_final: 0.7560 (ptt90) REVERT: E 219 LYS cc_start: 0.8141 (mtpm) cc_final: 0.7865 (mtpt) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.4895 time to fit residues: 19.4441 Evaluate side-chains 39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 0.1980 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.091375 restraints weight = 1592.964| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.28 r_work: 0.2980 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2295 Z= 0.187 Angle : 0.641 8.071 3080 Z= 0.342 Chirality : 0.038 0.126 275 Planarity : 0.003 0.016 445 Dihedral : 4.523 15.718 295 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 7.50 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.010 0.002 TYR E 101 PHE 0.011 0.002 PHE C 92 HIS 0.002 0.001 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 2295) covalent geometry : angle 0.64116 ( 3080) hydrogen bonds : bond 0.05087 ( 46) hydrogen bonds : angle 5.88763 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.054 Fit side-chains REVERT: B 98 ARG cc_start: 0.8152 (ptt90) cc_final: 0.7860 (ptt-90) REVERT: C 98 ARG cc_start: 0.7977 (ptt90) cc_final: 0.7640 (ptt-90) REVERT: C 219 LYS cc_start: 0.8016 (tttp) cc_final: 0.7395 (mttp) REVERT: E 219 LYS cc_start: 0.8111 (mtpm) cc_final: 0.7846 (mtpt) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.3935 time to fit residues: 17.6609 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 15 optimal weight: 5.9990 chunk 4 optimal weight: 30.0000 chunk 12 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091820 restraints weight = 1560.229| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.26 r_work: 0.2990 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2295 Z= 0.166 Angle : 0.622 7.379 3080 Z= 0.332 Chirality : 0.038 0.126 275 Planarity : 0.003 0.017 445 Dihedral : 4.512 15.366 295 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.25 % Allowed : 8.33 % Favored : 90.42 % 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: -3.91 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 98 TYR 0.010 0.002 TYR E 101 PHE 0.011 0.002 PHE C 92 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2295) covalent geometry : angle 0.62175 ( 3080) hydrogen bonds : bond 0.04759 ( 46) hydrogen bonds : angle 5.84223 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.062 Fit side-chains REVERT: B 98 ARG cc_start: 0.8164 (ptt90) cc_final: 0.7864 (ptt-90) REVERT: C 98 ARG cc_start: 0.7972 (ptt90) cc_final: 0.7633 (ptt-90) REVERT: C 219 LYS cc_start: 0.8026 (tttp) cc_final: 0.7395 (mttp) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.4154 time to fit residues: 17.8046 Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain C residue 125 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.091748 restraints weight = 1605.456| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.28 r_work: 0.2991 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2295 Z= 0.153 Angle : 0.622 7.166 3080 Z= 0.328 Chirality : 0.038 0.126 275 Planarity : 0.003 0.015 445 Dihedral : 4.503 15.158 295 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.08 % Allowed : 7.08 % Favored : 90.83 % 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: -3.91 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 98 TYR 0.010 0.002 TYR E 101 PHE 0.011 0.002 PHE C 92 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 2295) covalent geometry : angle 0.62236 ( 3080) hydrogen bonds : bond 0.04598 ( 46) hydrogen bonds : angle 5.81222 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.055 Fit side-chains REVERT: B 95 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8492 (mt0) REVERT: B 98 ARG cc_start: 0.8143 (ptt90) cc_final: 0.7814 (ptt-90) REVERT: C 98 ARG cc_start: 0.7939 (ptt90) cc_final: 0.7598 (ptt-90) REVERT: C 219 LYS cc_start: 0.8063 (tttp) cc_final: 0.7479 (mttt) REVERT: E 219 LYS cc_start: 0.8080 (mtpm) cc_final: 0.7597 (ttpp) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.6245 time to fit residues: 26.6821 Evaluate side-chains 44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain E residue 218 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 0.0010 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 226 ASN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096620 restraints weight = 1574.243| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.67 r_work: 0.2995 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2295 Z= 0.094 Angle : 0.565 6.931 3080 Z= 0.291 Chirality : 0.037 0.126 275 Planarity : 0.002 0.010 445 Dihedral : 4.247 13.993 295 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.25 % Allowed : 8.33 % Favored : 90.42 % 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: -3.89 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.17), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 98 TYR 0.009 0.001 TYR E 101 PHE 0.012 0.002 PHE C 92 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 2295) covalent geometry : angle 0.56468 ( 3080) hydrogen bonds : bond 0.03440 ( 46) hydrogen bonds : angle 5.66157 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 520 Ramachandran restraints generated. 260 Oldfield, 0 Emsley, 260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.089 Fit side-chains REVERT: B 98 ARG cc_start: 0.8128 (ptt90) cc_final: 0.7847 (ptt-90) REVERT: C 98 ARG cc_start: 0.7893 (ptt90) cc_final: 0.7531 (ptt-90) REVERT: C 219 LYS cc_start: 0.8040 (tttp) cc_final: 0.7423 (mttp) REVERT: D 219 LYS cc_start: 0.8302 (tttt) cc_final: 0.7501 (tptm) REVERT: E 219 LYS cc_start: 0.8118 (mtpm) cc_final: 0.7605 (ttpt) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.4980 time to fit residues: 20.8410 Evaluate side-chains 41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain C residue 125 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 17 optimal weight: 0.0980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 228 ASN C 122 GLN E 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.141221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091531 restraints weight = 1609.482| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.28 r_work: 0.2986 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2295 Z= 0.164 Angle : 0.635 7.676 3080 Z= 0.335 Chirality : 0.038 0.127 275 Planarity : 0.003 0.015 445 Dihedral : 4.513 15.017 295 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.25 % Allowed : 8.33 % Favored : 90.42 % 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: -3.90 (0.23), residues: 260 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.18), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 98 TYR 0.010 0.002 TYR E 101 PHE 0.011 0.002 PHE C 92 HIS 0.001 0.000 HIS E 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 2295) covalent geometry : angle 0.63526 ( 3080) hydrogen bonds : bond 0.04703 ( 46) hydrogen bonds : angle 5.78239 ( 138) =============================================================================== Job complete usr+sys time: 1001.08 seconds wall clock time: 17 minutes 44.65 seconds (1064.65 seconds total)