Starting phenix.real_space_refine on Tue Aug 4 20:52:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0g_65504/08_2026/9w0g_65504.map" } resolution = 2.0 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= 0.008 sd= 0.051 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 41 5.16 5 C 4162 2.51 5 N 1104 2.21 5 O 1265 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6572 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2300 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1880 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1904 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 231} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 297 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "G" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.57, per 1000 atoms: 0.24 Number of scatterers: 6572 At special positions: 0 Unit cell: (93.1, 109.858, 83.79, 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 41 16.00 O 1265 8.00 N 1104 7.00 C 4162 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 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " GAL G 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... BETA2-6 " GAL G 2 " - " SIA G 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... Time building additional restraints: 0.55 Conformation dependent library (CDL) restraints added in 447.0 milliseconds 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.9% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 54 through 57 removed outlier: 3.564A pdb=" N THR A 57 " --> pdb=" O VAL A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 100 through 109 removed outlier: 3.667A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.748A pdb=" N SER A 165 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.567A pdb=" N ALA B 47 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 89 through 98 Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.124A pdb=" N MET C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.711A pdb=" N ARG C 68 " --> pdb=" O GLU C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 104 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'D' and resid 34 through 38 Processing helix chain 'D' and resid 49 through 54 Processing helix chain 'E' and resid 201 through 205 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 76 removed outlier: 5.647A pdb=" N LEU A 68 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET A 241 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 184 removed outlier: 4.945A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA A 248 " --> pdb=" O ILE C 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 90 through 94 Processing sheet with id=AA7, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA8, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.914A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.914A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.589A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.878A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.261A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 522 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: 0.91 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2116 1.34 - 1.46: 1257 1.46 - 1.57: 3293 1.57 - 1.69: 1 1.69 - 1.81: 68 Bond restraints: 6735 Sorted by residual: bond pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CA ARG E 205 " pdb=" CB ARG E 205 " ideal model delta sigma weight residual 1.532 1.545 -0.013 1.51e-02 4.39e+03 7.55e-01 bond pdb=" C GLN B 119 " pdb=" N GLY B 120 " ideal model delta sigma weight residual 1.319 1.330 -0.011 1.34e-02 5.57e+03 7.08e-01 bond pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.90e-01 bond pdb=" N ASN A 130 " pdb=" CA ASN A 130 " ideal model delta sigma weight residual 1.460 1.470 -0.010 1.54e-02 4.22e+03 4.41e-01 ... (remaining 6730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 8853 1.14 - 2.27: 239 2.27 - 3.41: 79 3.41 - 4.54: 3 4.54 - 5.68: 7 Bond angle restraints: 9181 Sorted by residual: angle pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 112.60 117.20 -4.60 1.70e+00 3.46e-01 7.33e+00 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 119.18 -5.08 2.00e+00 2.50e-01 6.45e+00 angle pdb=" CA ARG E 205 " pdb=" CB ARG E 205 " pdb=" CG ARG E 205 " ideal model delta sigma weight residual 114.10 119.07 -4.97 2.00e+00 2.50e-01 6.17e+00 angle pdb=" N ILE B 246 " pdb=" CA ILE B 246 " pdb=" C ILE B 246 " ideal model delta sigma weight residual 110.62 112.94 -2.32 1.02e+00 9.61e-01 5.17e+00 angle pdb=" N SER A 167 " pdb=" CA SER A 167 " pdb=" C SER A 167 " ideal model delta sigma weight residual 114.04 111.26 2.78 1.24e+00 6.50e-01 5.03e+00 ... (remaining 9176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 3810 21.88 - 43.75: 235 43.75 - 65.63: 54 65.63 - 87.50: 13 87.50 - 109.38: 9 Dihedral angle restraints: 4121 sinusoidal: 1719 harmonic: 2402 Sorted by residual: dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" C5 MAN F 4 " ideal model delta sinusoidal sigma weight residual 54.75 -54.63 109.38 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" C2 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O4 MAN F 4 " ideal model delta sinusoidal sigma weight residual 176.13 67.31 108.82 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C5 MAN F 4 " pdb=" C3 MAN F 4 " pdb=" C4 MAN F 4 " pdb=" O3 MAN F 4 " ideal model delta sinusoidal sigma weight residual -174.53 -66.65 -107.88 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 4118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 838 0.047 - 0.093: 161 0.093 - 0.140: 59 0.140 - 0.186: 3 0.186 - 0.233: 1 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C2 SIA G 3 " pdb=" O6 GAL G 2 " pdb=" C1 SIA G 3 " pdb=" O6 SIA G 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.47 -0.03 2.00e-02 2.50e+03 1.62e+00 chirality pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" O3 BMA F 3 " both_signs ideal model delta sigma weight residual False 2.41 2.17 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.12 -0.15 2.00e-01 2.50e+01 5.93e-01 ... (remaining 1059 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 31 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO C 32 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 32 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 32 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 205 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C ARG E 205 " 0.020 2.00e-02 2.50e+03 pdb=" O ARG E 205 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU E 206 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 134 " 0.006 2.00e-02 2.50e+03 1.12e-02 1.26e+00 pdb=" C THR A 134 " -0.019 2.00e-02 2.50e+03 pdb=" O THR A 134 " 0.007 2.00e-02 2.50e+03 pdb=" N TYR A 135 " 0.006 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.01: 3538 3.01 - 3.48: 6147 3.48 - 3.95: 11223 3.95 - 4.43: 13268 4.43 - 4.90: 20679 Nonbonded interactions: 54855 Sorted by model distance: nonbonded pdb=" C6 GAL G 2 " pdb=" O6 SIA G 3 " model vdw 2.534 2.752 nonbonded pdb=" O5 BMA F 3 " pdb=" O6 BMA F 3 " model vdw 2.553 2.432 nonbonded pdb=" C4 NAG G 1 " pdb=" O5 GAL G 2 " model vdw 2.586 2.776 nonbonded pdb=" C3 MAN F 4 " pdb=" O5 MAN F 4 " model vdw 2.589 2.776 nonbonded pdb=" N GLU A 19 " pdb=" OE1 GLU A 19 " model vdw 2.606 3.120 ... (remaining 54850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.690 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:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 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 0.032 6742 Z= 0.107 Angle : 0.517 5.678 9202 Z= 0.273 Chirality : 0.042 0.233 1062 Planarity : 0.004 0.029 1173 Dihedral : 16.260 109.381 2569 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.12 % Allowed : 15.38 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.20 (0.29), residues: 819 helix: -1.66 (0.62), residues: 66 sheet: 0.79 (0.38), residues: 189 loop : -0.23 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 12 TYR 0.014 0.001 TYR B 31 PHE 0.007 0.001 PHE A 100 TRP 0.007 0.001 TRP B 207 HIS 0.002 0.000 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 6735) covalent geometry : angle 0.50744 / 0.27 ( 9181) hydrogen bonds : bond 0.16991 / 12.13 ( 177) hydrogen bonds : angle 8.59836 / 5.73 ( 522) glycosidic custom : bond 0.00081 / 0.04 ( 1) glycosidic custom : angle 0.60914 / 0.30 ( 3) link_ALPHA1-3 : bond 0.00452 / 0.24 ( 1) link_ALPHA1-3 : angle 3.48463 / 1.78 ( 3) link_ALPHA1-6 : bond 0.00792 / 0.42 ( 1) link_ALPHA1-6 : angle 1.40704 / 0.79 ( 3) link_BETA1-4 : bond 0.00631 / 0.25 ( 3) link_BETA1-4 : angle 2.36523 / 1.26 ( 9) link_BETA1-6 : bond 0.00424 / 0.22 ( 1) link_BETA1-6 : angle 1.20746 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.286 Fit side-chains REVERT: A 51 GLN cc_start: 0.9424 (mt0) cc_final: 0.9194 (mt0) REVERT: A 136 MET cc_start: 0.4683 (ttt) cc_final: 0.3794 (mtp) REVERT: A 295 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8990 (m) REVERT: B 67 ARG cc_start: 0.8669 (mtm110) cc_final: 0.8160 (ptp-110) REVERT: C 53 MET cc_start: 0.9461 (mtm) cc_final: 0.9071 (mtm) REVERT: C 74 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8886 (mm-40) REVERT: C 145 GLU cc_start: 0.8459 (pm20) cc_final: 0.8065 (pm20) outliers start: 8 outliers final: 7 residues processed: 110 average time/residue: 0.5863 time to fit residues: 67.4693 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 17 ASN A 44 GLN B 45 HIS B 131 GLN B 206 GLN B 240 ASN C 101 ASN C 160 GLN C 186 ASN C 235 GLN D 30 ASN E 200 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.089372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.072909 restraints weight = 9245.372| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.84 r_work: 0.2798 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.0613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6742 Z= 0.113 Angle : 0.518 8.239 9202 Z= 0.260 Chirality : 0.044 0.206 1062 Planarity : 0.004 0.027 1173 Dihedral : 9.206 80.820 1088 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.10 % Allowed : 14.69 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.15 (0.29), residues: 819 helix: -1.55 (0.64), residues: 61 sheet: 0.79 (0.37), residues: 197 loop : -0.22 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.015 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.003 0.001 HIS A 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 6735) covalent geometry : angle 0.51075 / 0.26 ( 9181) hydrogen bonds : bond 0.03554 / 2.45 ( 177) hydrogen bonds : angle 6.24770 / 4.21 ( 522) glycosidic custom : bond 0.00035 / 0.02 ( 1) glycosidic custom : angle 0.78613 / 0.39 ( 3) link_ALPHA1-3 : bond 0.00651 / 0.34 ( 1) link_ALPHA1-3 : angle 2.57175 / 1.32 ( 3) link_ALPHA1-6 : bond 0.00617 / 0.32 ( 1) link_ALPHA1-6 : angle 1.39319 / 0.78 ( 3) link_BETA1-4 : bond 0.00620 / 0.24 ( 3) link_BETA1-4 : angle 2.28942 / 1.22 ( 9) link_BETA1-6 : bond 0.00413 / 0.22 ( 1) link_BETA1-6 : angle 1.14341 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.265 Fit side-chains REVERT: A 2 GLU cc_start: 0.8449 (tt0) cc_final: 0.8195 (tt0) REVERT: A 51 GLN cc_start: 0.9431 (mt0) cc_final: 0.9170 (mt0) REVERT: A 136 MET cc_start: 0.4754 (ttt) cc_final: 0.3799 (mtp) REVERT: A 295 VAL cc_start: 0.9201 (p) cc_final: 0.8987 (m) REVERT: B 67 ARG cc_start: 0.8654 (mtm110) cc_final: 0.8252 (ptp-110) REVERT: B 72 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8491 (mm-30) REVERT: B 148 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8482 (mptp) REVERT: C 53 MET cc_start: 0.9476 (mtm) cc_final: 0.9085 (mtm) REVERT: C 74 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8966 (mm-40) REVERT: C 145 GLU cc_start: 0.8477 (pm20) cc_final: 0.8052 (pm20) REVERT: E 205 ARG cc_start: 0.8830 (ppt170) cc_final: 0.8612 (ppp-140) outliers start: 15 outliers final: 8 residues processed: 105 average time/residue: 0.4728 time to fit residues: 52.1601 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 68 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN C 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.086413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.069805 restraints weight = 9155.406| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.84 r_work: 0.2746 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6742 Z= 0.229 Angle : 0.571 5.335 9202 Z= 0.293 Chirality : 0.046 0.199 1062 Planarity : 0.004 0.049 1173 Dihedral : 7.494 80.689 1079 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.52 % Allowed : 13.57 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.23 (0.28), residues: 819 helix: -1.57 (0.62), residues: 66 sheet: 0.84 (0.37), residues: 190 loop : -0.30 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 205 TYR 0.020 0.002 TYR B 31 PHE 0.012 0.002 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 ( 6735) covalent geometry : angle 0.56293 / 0.29 ( 9181) hydrogen bonds : bond 0.04223 / 2.95 ( 177) hydrogen bonds : angle 6.18074 / 4.19 ( 522) glycosidic custom : bond 0.00067 / 0.04 ( 1) glycosidic custom : angle 0.84092 / 0.41 ( 3) link_ALPHA1-3 : bond 0.00046 / 0.02 ( 1) link_ALPHA1-3 : angle 3.03996 / 1.59 ( 3) link_ALPHA1-6 : bond 0.00515 / 0.27 ( 1) link_ALPHA1-6 : angle 1.46793 / 0.83 ( 3) link_BETA1-4 : bond 0.00598 / 0.24 ( 3) link_BETA1-4 : angle 2.33502 / 1.18 ( 9) link_BETA1-6 : bond 0.00246 / 0.13 ( 1) link_BETA1-6 : angle 1.11100 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.260 Fit side-chains REVERT: A 2 GLU cc_start: 0.8495 (tt0) cc_final: 0.8236 (tt0) REVERT: A 51 GLN cc_start: 0.9451 (mt0) cc_final: 0.9213 (mt0) REVERT: A 136 MET cc_start: 0.4771 (ttt) cc_final: 0.3768 (mtp) REVERT: A 295 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8978 (m) REVERT: B 148 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8587 (mptp) REVERT: C 53 MET cc_start: 0.9525 (mtm) cc_final: 0.9205 (mtm) REVERT: C 145 GLU cc_start: 0.8506 (pm20) cc_final: 0.8120 (pm20) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 0.5995 time to fit residues: 65.9174 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 34 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.087374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.070877 restraints weight = 9233.230| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.83 r_work: 0.2763 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9012 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6742 Z= 0.164 Angle : 0.530 5.109 9202 Z= 0.272 Chirality : 0.044 0.204 1062 Planarity : 0.004 0.036 1173 Dihedral : 7.246 80.413 1079 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 13.85 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.18 (0.28), residues: 819 helix: -1.49 (0.62), residues: 66 sheet: 0.90 (0.37), residues: 189 loop : -0.27 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 12 TYR 0.018 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 ( 6735) covalent geometry : angle 0.52077 / 0.27 ( 9181) hydrogen bonds : bond 0.03699 / 2.56 ( 177) hydrogen bonds : angle 5.96756 / 4.04 ( 522) glycosidic custom : bond 0.00103 / 0.05 ( 1) glycosidic custom : angle 0.83180 / 0.42 ( 3) link_ALPHA1-3 : bond 0.00103 / 0.05 ( 1) link_ALPHA1-3 : angle 3.48320 / 1.80 ( 3) link_ALPHA1-6 : bond 0.00595 / 0.31 ( 1) link_ALPHA1-6 : angle 1.43431 / 0.81 ( 3) link_BETA1-4 : bond 0.00564 / 0.22 ( 3) link_BETA1-4 : angle 2.20990 / 1.14 ( 9) link_BETA1-6 : bond 0.00295 / 0.16 ( 1) link_BETA1-6 : angle 1.13760 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.255 Fit side-chains REVERT: A 2 GLU cc_start: 0.8464 (tt0) cc_final: 0.8185 (tt0) REVERT: A 51 GLN cc_start: 0.9451 (mt0) cc_final: 0.9208 (mt0) REVERT: A 136 MET cc_start: 0.4914 (ttt) cc_final: 0.3897 (mtp) REVERT: A 295 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8970 (m) REVERT: B 148 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8475 (mptp) REVERT: C 53 MET cc_start: 0.9518 (mtm) cc_final: 0.9183 (mtm) REVERT: C 145 GLU cc_start: 0.8511 (pm20) cc_final: 0.8118 (pm20) outliers start: 17 outliers final: 13 residues processed: 106 average time/residue: 0.5913 time to fit residues: 65.7594 Evaluate side-chains 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 77 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.070311 restraints weight = 9365.374| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.84 r_work: 0.2751 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6742 Z= 0.192 Angle : 0.549 5.246 9202 Z= 0.282 Chirality : 0.045 0.218 1062 Planarity : 0.004 0.042 1173 Dihedral : 7.282 80.376 1079 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 14.41 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.21 (0.28), residues: 819 helix: -1.53 (0.61), residues: 66 sheet: 0.86 (0.37), residues: 190 loop : -0.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 12 TYR 0.019 0.002 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.007 0.001 TRP A 249 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 6735) covalent geometry : angle 0.54111 / 0.28 ( 9181) hydrogen bonds : bond 0.03802 / 2.64 ( 177) hydrogen bonds : angle 5.95723 / 4.04 ( 522) glycosidic custom : bond 0.00036 / 0.02 ( 1) glycosidic custom : angle 0.87089 / 0.43 ( 3) link_ALPHA1-3 : bond 0.00083 / 0.04 ( 1) link_ALPHA1-3 : angle 3.47614 / 1.78 ( 3) link_ALPHA1-6 : bond 0.00561 / 0.30 ( 1) link_ALPHA1-6 : angle 1.42356 / 0.80 ( 3) link_BETA1-4 : bond 0.00580 / 0.22 ( 3) link_BETA1-4 : angle 2.10266 / 1.08 ( 9) link_BETA1-6 : bond 0.00221 / 0.12 ( 1) link_BETA1-6 : angle 1.14276 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.317 Fit side-chains REVERT: A 2 GLU cc_start: 0.8451 (tt0) cc_final: 0.8169 (tt0) REVERT: A 51 GLN cc_start: 0.9450 (mt0) cc_final: 0.9215 (mt0) REVERT: A 136 MET cc_start: 0.4916 (ttt) cc_final: 0.3985 (mtp) REVERT: A 295 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8959 (m) REVERT: B 148 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8502 (mptp) REVERT: C 53 MET cc_start: 0.9522 (mtm) cc_final: 0.9214 (mtm) REVERT: C 74 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8971 (mm-40) REVERT: C 145 GLU cc_start: 0.8518 (pm20) cc_final: 0.8070 (pm20) REVERT: C 148 MET cc_start: 0.8184 (ppp) cc_final: 0.7819 (pp-130) REVERT: E 205 ARG cc_start: 0.8762 (ppt170) cc_final: 0.8537 (ppp-140) outliers start: 17 outliers final: 13 residues processed: 107 average time/residue: 0.6251 time to fit residues: 70.1173 Evaluate side-chains 109 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 226 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 64 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.072526 restraints weight = 9199.969| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.84 r_work: 0.2789 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6742 Z= 0.107 Angle : 0.496 5.652 9202 Z= 0.252 Chirality : 0.042 0.214 1062 Planarity : 0.004 0.033 1173 Dihedral : 7.060 80.301 1079 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.96 % Allowed : 15.10 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.11 (0.29), residues: 819 helix: -1.42 (0.64), residues: 66 sheet: 0.93 (0.37), residues: 189 loop : -0.23 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 12 TYR 0.015 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP B 207 HIS 0.002 0.000 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 6735) covalent geometry : angle 0.48742 / 0.25 ( 9181) hydrogen bonds : bond 0.03159 / 2.16 ( 177) hydrogen bonds : angle 5.69305 / 3.86 ( 522) glycosidic custom : bond 0.00160 / 0.08 ( 1) glycosidic custom : angle 0.76682 / 0.39 ( 3) link_ALPHA1-3 : bond 0.00086 / 0.05 ( 1) link_ALPHA1-3 : angle 3.49068 / 1.79 ( 3) link_ALPHA1-6 : bond 0.00628 / 0.33 ( 1) link_ALPHA1-6 : angle 1.40660 / 0.78 ( 3) link_BETA1-4 : bond 0.00587 / 0.22 ( 3) link_BETA1-4 : angle 1.99135 / 1.05 ( 9) link_BETA1-6 : bond 0.00313 / 0.16 ( 1) link_BETA1-6 : angle 1.17066 / 0.59 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.273 Fit side-chains REVERT: A 2 GLU cc_start: 0.8444 (tt0) cc_final: 0.8162 (tt0) REVERT: A 51 GLN cc_start: 0.9446 (mt0) cc_final: 0.9206 (mt0) REVERT: A 136 MET cc_start: 0.4748 (ttt) cc_final: 0.3852 (mtp) REVERT: A 295 VAL cc_start: 0.9182 (OUTLIER) cc_final: 0.8976 (m) REVERT: B 72 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8528 (mm-30) REVERT: B 148 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8446 (mptp) REVERT: C 53 MET cc_start: 0.9481 (mtm) cc_final: 0.9159 (mtm) REVERT: C 74 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8927 (mm-40) REVERT: C 145 GLU cc_start: 0.8486 (pm20) cc_final: 0.8093 (pm20) REVERT: C 159 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.9051 (mt) REVERT: E 205 ARG cc_start: 0.8686 (ppt170) cc_final: 0.8249 (ppt170) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.6495 time to fit residues: 71.3722 Evaluate side-chains 107 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 0.0670 chunk 50 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.086843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.070303 restraints weight = 9163.946| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.83 r_work: 0.2751 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6742 Z= 0.205 Angle : 0.555 5.664 9202 Z= 0.284 Chirality : 0.045 0.224 1062 Planarity : 0.004 0.044 1173 Dihedral : 7.203 80.344 1078 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.52 % Allowed : 14.55 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.21 (0.28), residues: 819 helix: -1.53 (0.61), residues: 66 sheet: 0.85 (0.37), residues: 190 loop : -0.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 12 TYR 0.020 0.002 TYR B 31 PHE 0.012 0.002 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.005 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 ( 6735) covalent geometry : angle 0.54681 / 0.28 ( 9181) hydrogen bonds : bond 0.03789 / 2.63 ( 177) hydrogen bonds : angle 5.91670 / 4.02 ( 522) glycosidic custom : bond 0.00014 / 0.01 ( 1) glycosidic custom : angle 0.87267 / 0.43 ( 3) link_ALPHA1-3 : bond 0.00058 / 0.03 ( 1) link_ALPHA1-3 : angle 3.45536 / 1.77 ( 3) link_ALPHA1-6 : bond 0.00539 / 0.28 ( 1) link_ALPHA1-6 : angle 1.42276 / 0.79 ( 3) link_BETA1-4 : bond 0.00579 / 0.23 ( 3) link_BETA1-4 : angle 2.00076 / 1.02 ( 9) link_BETA1-6 : bond 0.00189 / 0.10 ( 1) link_BETA1-6 : angle 1.16313 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.255 Fit side-chains REVERT: A 2 GLU cc_start: 0.8462 (tt0) cc_final: 0.8176 (tt0) REVERT: A 51 GLN cc_start: 0.9449 (mt0) cc_final: 0.9176 (mt0) REVERT: A 136 MET cc_start: 0.4649 (ttt) cc_final: 0.3746 (mtp) REVERT: A 295 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8958 (m) REVERT: B 148 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8594 (mptp) REVERT: C 53 MET cc_start: 0.9524 (mtm) cc_final: 0.9226 (mtm) REVERT: C 145 GLU cc_start: 0.8517 (pm20) cc_final: 0.8132 (pm20) REVERT: C 159 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9062 (mt) outliers start: 18 outliers final: 9 residues processed: 106 average time/residue: 0.5939 time to fit residues: 66.0099 Evaluate side-chains 104 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 61 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.090915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.074580 restraints weight = 9223.249| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.83 r_work: 0.2829 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6742 Z= 0.084 Angle : 0.485 6.470 9202 Z= 0.244 Chirality : 0.042 0.209 1062 Planarity : 0.004 0.029 1173 Dihedral : 6.868 80.304 1078 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 14.97 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.10 (0.28), residues: 819 helix: -1.42 (0.64), residues: 61 sheet: 0.82 (0.37), residues: 197 loop : -0.20 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.012 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.008 0.001 TRP A 93 HIS 0.002 0.000 HIS B 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.08 ( 6735) covalent geometry : angle 0.47624 / 0.24 ( 9181) hydrogen bonds : bond 0.02852 / 1.92 ( 177) hydrogen bonds : angle 5.44608 / 3.70 ( 522) glycosidic custom : bond 0.00265 / 0.14 ( 1) glycosidic custom : angle 0.71771 / 0.37 ( 3) link_ALPHA1-3 : bond 0.00215 / 0.11 ( 1) link_ALPHA1-3 : angle 3.43970 / 1.77 ( 3) link_ALPHA1-6 : bond 0.00647 / 0.34 ( 1) link_ALPHA1-6 : angle 1.42349 / 0.79 ( 3) link_BETA1-4 : bond 0.00627 / 0.24 ( 3) link_BETA1-4 : angle 1.87523 / 1.00 ( 9) link_BETA1-6 : bond 0.00340 / 0.18 ( 1) link_BETA1-6 : angle 1.16471 / 0.60 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.255 Fit side-chains REVERT: A 2 GLU cc_start: 0.8420 (tt0) cc_final: 0.8106 (tt0) REVERT: A 51 GLN cc_start: 0.9438 (mt0) cc_final: 0.9187 (mt0) REVERT: A 136 MET cc_start: 0.4664 (ttt) cc_final: 0.3810 (mtp) REVERT: A 295 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8956 (m) REVERT: B 72 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8538 (mm-30) REVERT: B 148 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8456 (mptp) REVERT: C 53 MET cc_start: 0.9429 (mtm) cc_final: 0.9155 (mtm) REVERT: C 74 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8917 (mm-40) REVERT: C 145 GLU cc_start: 0.8474 (pm20) cc_final: 0.8093 (pm20) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 0.6233 time to fit residues: 71.2002 Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 17 optimal weight: 0.3980 chunk 51 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.072477 restraints weight = 9172.955| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.85 r_work: 0.2794 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6742 Z= 0.122 Angle : 0.506 6.039 9202 Z= 0.256 Chirality : 0.042 0.212 1062 Planarity : 0.004 0.028 1173 Dihedral : 6.862 80.508 1078 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.26 % Allowed : 15.52 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.07 (0.29), residues: 819 helix: -1.49 (0.62), residues: 67 sheet: 0.89 (0.37), residues: 197 loop : -0.17 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 12 TYR 0.017 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP C 155 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6735) covalent geometry : angle 0.49770 / 0.25 ( 9181) hydrogen bonds : bond 0.03178 / 2.19 ( 177) hydrogen bonds : angle 5.55337 / 3.78 ( 522) glycosidic custom : bond 0.00110 / 0.06 ( 1) glycosidic custom : angle 0.79298 / 0.39 ( 3) link_ALPHA1-3 : bond 0.00160 / 0.08 ( 1) link_ALPHA1-3 : angle 3.38554 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00577 / 0.30 ( 1) link_ALPHA1-6 : angle 1.40131 / 0.78 ( 3) link_BETA1-4 : bond 0.00557 / 0.21 ( 3) link_BETA1-4 : angle 1.85693 / 0.96 ( 9) link_BETA1-6 : bond 0.00274 / 0.14 ( 1) link_BETA1-6 : angle 1.19332 / 0.61 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.276 Fit side-chains REVERT: A 2 GLU cc_start: 0.8440 (tt0) cc_final: 0.8177 (tt0) REVERT: A 51 GLN cc_start: 0.9450 (mt0) cc_final: 0.9210 (mt0) REVERT: A 136 MET cc_start: 0.4717 (ttt) cc_final: 0.3806 (ttp) REVERT: A 295 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8967 (m) REVERT: B 148 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8488 (mptp) REVERT: C 53 MET cc_start: 0.9473 (mtm) cc_final: 0.9181 (mtm) REVERT: C 74 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8899 (mm-40) REVERT: C 145 GLU cc_start: 0.8489 (pm20) cc_final: 0.8095 (pm20) REVERT: C 159 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9051 (mt) outliers start: 9 outliers final: 6 residues processed: 102 average time/residue: 0.6362 time to fit residues: 67.9370 Evaluate side-chains 103 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 16 optimal weight: 0.0770 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN E 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.087775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.071095 restraints weight = 9174.347| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 1.86 r_work: 0.2769 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6742 Z= 0.166 Angle : 0.537 5.993 9202 Z= 0.274 Chirality : 0.044 0.218 1062 Planarity : 0.004 0.037 1173 Dihedral : 6.987 80.296 1078 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.40 % Allowed : 15.52 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.13 (0.28), residues: 819 helix: -1.53 (0.62), residues: 67 sheet: 0.94 (0.37), residues: 190 loop : -0.24 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.018 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.007 0.001 TRP C 155 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 6735) covalent geometry : angle 0.52934 / 0.27 ( 9181) hydrogen bonds : bond 0.03517 / 2.43 ( 177) hydrogen bonds : angle 5.70600 / 3.88 ( 522) glycosidic custom : bond 0.00057 / 0.03 ( 1) glycosidic custom : angle 0.82690 / 0.41 ( 3) link_ALPHA1-3 : bond 0.00068 / 0.04 ( 1) link_ALPHA1-3 : angle 3.38566 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00536 / 0.28 ( 1) link_ALPHA1-6 : angle 1.41181 / 0.78 ( 3) link_BETA1-4 : bond 0.00551 / 0.21 ( 3) link_BETA1-4 : angle 1.86068 / 0.95 ( 9) link_BETA1-6 : bond 0.00221 / 0.12 ( 1) link_BETA1-6 : angle 1.18954 / 0.61 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1638 Ramachandran restraints generated. 819 Oldfield, 0 Emsley, 819 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.272 Fit side-chains REVERT: A 2 GLU cc_start: 0.8451 (tt0) cc_final: 0.8180 (tt0) REVERT: A 51 GLN cc_start: 0.9452 (mt0) cc_final: 0.9218 (mt0) REVERT: A 136 MET cc_start: 0.4629 (ttt) cc_final: 0.3745 (ttp) REVERT: A 295 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (m) REVERT: B 148 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8558 (mptp) REVERT: C 53 MET cc_start: 0.9514 (mtm) cc_final: 0.9232 (mtm) REVERT: C 74 GLN cc_start: 0.9201 (mm-40) cc_final: 0.8943 (mm-40) REVERT: C 145 GLU cc_start: 0.8492 (pm20) cc_final: 0.8098 (pm20) REVERT: C 159 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9058 (mt) outliers start: 10 outliers final: 7 residues processed: 99 average time/residue: 0.6140 time to fit residues: 63.6740 Evaluate side-chains 101 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 164 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.087951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.071386 restraints weight = 9216.434| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.85 r_work: 0.2773 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6742 Z= 0.151 Angle : 0.526 5.806 9202 Z= 0.268 Chirality : 0.044 0.217 1062 Planarity : 0.004 0.032 1173 Dihedral : 6.978 80.088 1078 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.40 % Allowed : 15.66 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.13 (0.28), residues: 819 helix: -1.53 (0.62), residues: 67 sheet: 0.98 (0.37), residues: 189 loop : -0.25 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 12 TYR 0.018 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.006 0.001 TRP C 155 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6735) covalent geometry : angle 0.51832 / 0.27 ( 9181) hydrogen bonds : bond 0.03414 / 2.35 ( 177) hydrogen bonds : angle 5.68859 / 3.87 ( 522) glycosidic custom : bond 0.00096 / 0.05 ( 1) glycosidic custom : angle 0.80861 / 0.40 ( 3) link_ALPHA1-3 : bond 0.00076 / 0.04 ( 1) link_ALPHA1-3 : angle 3.38587 / 1.74 ( 3) link_ALPHA1-6 : bond 0.00554 / 0.29 ( 1) link_ALPHA1-6 : angle 1.41250 / 0.78 ( 3) link_BETA1-4 : bond 0.00550 / 0.21 ( 3) link_BETA1-4 : angle 1.82061 / 0.94 ( 9) link_BETA1-6 : bond 0.00234 / 0.12 ( 1) link_BETA1-6 : angle 1.20192 / 0.61 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3234.23 seconds wall clock time: 55 minutes 43.48 seconds (3343.48 seconds total)