Starting phenix.real_space_refine on Thu Oct 22 23:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.cif Found real_map, /net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.map" model { file = "/net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23bg_68830/10_2026/23bg_68830.cif" } resolution = 2.47 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= 0.009 sd= 0.043 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 37 5.16 5 C 4161 2.51 5 N 1103 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 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6566 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2312 Classifications: {'peptide': 296} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 278} Chain: "B" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1870 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1896 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: 1.54, per 1000 atoms: 0.23 Number of scatterers: 6566 At special positions: 0 Unit cell: (105.203, 84.721, 84.721, 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 37 16.00 O 1265 8.00 N 1103 7.00 C 4161 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: 0.48 Conformation dependent library (CDL) restraints added in 358.7 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: 1554 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 12 sheets defined 15.7% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 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: 3.505A 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 108 Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.689A 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 56 through 60 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 43 through 48 Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.712A pdb=" N LYS 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 242 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: 6.502A pdb=" N VAL A 239 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS A 71 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 237 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER A 73 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 235 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU A 75 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 233 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA C 22 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 193 through 194 removed outlier: 4.750A pdb=" N PHE A 110 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA A 250 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TYR A 112 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ALA A 248 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 114 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE A 246 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ALA A 248 " --> pdb=" O VAL 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: 6.805A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.457A 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: 6.805A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.596A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.076A 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 84 removed outlier: 6.914A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASN C 199 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 176 through 177 214 hydrogen bonds defined for protein. 510 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: 0.95 Time building geometry restraints manager: 0.64 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: 2115 1.34 - 1.46: 1159 1.46 - 1.57: 3393 1.57 - 1.69: 1 1.69 - 1.81: 60 Bond restraints: 6728 Sorted by residual: bond pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.78e+00 bond pdb=" CB GLU C 145 " pdb=" CG GLU C 145 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CG GLU C 145 " pdb=" CD GLU C 145 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.03e-01 bond pdb=" CG GLU A 19 " pdb=" CD GLU A 19 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 8.89e-01 bond pdb=" CB GLU A 271 " pdb=" CG GLU A 271 " ideal model delta sigma weight residual 1.520 1.547 -0.027 3.00e-02 1.11e+03 8.21e-01 ... (remaining 6723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 9025 1.92 - 3.84: 133 3.84 - 5.75: 13 5.75 - 7.67: 0 7.67 - 9.59: 2 Bond angle restraints: 9173 Sorted by residual: angle pdb=" N ILE C 88 " pdb=" CA ILE C 88 " pdb=" C ILE C 88 " ideal model delta sigma weight residual 112.29 106.76 5.53 9.40e-01 1.13e+00 3.46e+01 angle pdb=" N VAL B 48 " pdb=" CA VAL B 48 " pdb=" C VAL B 48 " ideal model delta sigma weight residual 111.62 109.04 2.58 7.90e-01 1.60e+00 1.07e+01 angle pdb=" CB MET A 187 " pdb=" CG MET A 187 " pdb=" SD MET A 187 " ideal model delta sigma weight residual 112.70 122.29 -9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 119.85 -5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" CA GLU C 145 " pdb=" CB GLU C 145 " pdb=" CG GLU C 145 " ideal model delta sigma weight residual 114.10 119.77 -5.67 2.00e+00 2.50e-01 8.04e+00 ... (remaining 9168 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 3777 21.87 - 43.73: 268 43.73 - 65.60: 52 65.60 - 87.47: 13 87.47 - 109.34: 9 Dihedral angle restraints: 4119 sinusoidal: 1716 harmonic: 2403 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 -54.59 109.34 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 67.51 108.62 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 -66.68 -107.85 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 4116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 825 0.046 - 0.093: 177 0.093 - 0.139: 59 0.139 - 0.186: 1 0.186 - 0.232: 2 Chirality restraints: 1064 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 -2.44 -0.06 2.00e-02 2.50e+03 8.40e+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 2.18 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU C 86 " pdb=" CB LEU C 86 " pdb=" CD1 LEU C 86 " pdb=" CD2 LEU C 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1061 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 31 " 0.011 2.00e-02 2.50e+03 8.30e-03 1.38e+00 pdb=" CG TYR B 31 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 31 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 31 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 31 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 31 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 31 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 30 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" CG ASN D 30 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN D 30 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN D 30 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 51 " -0.005 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" CG ASP B 51 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASP B 51 " -0.007 2.00e-02 2.50e+03 pdb=" OD2 ASP B 51 " -0.007 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3487 3.00 - 3.48: 6208 3.48 - 3.95: 11335 3.95 - 4.43: 13231 4.43 - 4.90: 20799 Nonbonded interactions: 55060 Sorted by model distance: nonbonded pdb=" O5 BMA F 3 " pdb=" O6 BMA F 3 " model vdw 2.525 2.432 nonbonded pdb=" N GLU C 145 " pdb=" OE1 GLU C 145 " model vdw 2.531 3.120 nonbonded pdb=" C6 GAL G 2 " pdb=" O6 SIA G 3 " model vdw 2.541 2.752 nonbonded pdb=" N GLU A 19 " pdb=" OE1 GLU A 19 " model vdw 2.541 3.120 nonbonded pdb=" N ILE C 88 " pdb=" N GLN C 89 " model vdw 2.544 2.560 ... (remaining 55055 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: 0.810 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:8.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6735 Z= 0.122 Angle : 0.566 9.590 9194 Z= 0.302 Chirality : 0.042 0.232 1064 Planarity : 0.003 0.027 1172 Dihedral : 16.446 109.336 2565 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.70 % Allowed : 14.89 % Favored : 84.41 % 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: -2.72 (0.50), residues: 67 sheet: 0.58 (0.37), residues: 201 loop : -0.03 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 272 TYR 0.020 0.001 TYR B 31 PHE 0.010 0.001 PHE C 222 TRP 0.008 0.001 TRP A 249 HIS 0.004 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 6728) covalent geometry : angle 0.55650 / 0.30 ( 9173) hydrogen bonds : bond 0.19047 / 12.36 ( 174) hydrogen bonds : angle 8.80017 / 6.02 ( 510) glycosidic custom : bond 0.00012 / 0.01 ( 1) glycosidic custom : angle 0.61651 / 0.25 ( 3) link_ALPHA1-3 : bond 0.00449 / 0.24 ( 1) link_ALPHA1-3 : angle 3.52295 / 1.65 ( 3) link_ALPHA1-6 : bond 0.00747 / 0.39 ( 1) link_ALPHA1-6 : angle 1.48702 / 0.81 ( 3) link_BETA1-4 : bond 0.00675 / 0.26 ( 3) link_BETA1-4 : angle 2.40424 / 1.11 ( 9) link_BETA1-6 : bond 0.00570 / 0.30 ( 1) link_BETA1-6 : angle 1.06964 / 0.45 ( 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 106 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.263 Fit side-chains REVERT: B 52 LYS cc_start: 0.9334 (tttm) cc_final: 0.7186 (mppt) REVERT: B 102 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 220 ASP cc_start: 0.8483 (p0) cc_final: 0.8075 (p0) outliers start: 5 outliers final: 4 residues processed: 104 average time/residue: 0.5453 time to fit residues: 59.6098 Evaluate side-chains 103 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 98 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain D residue 39 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.0570 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 GLN B 45 HIS B 55 GLN B 88 ASN B 97 GLN B 240 ASN C 101 ASN C 160 GLN C 247 GLN D 30 ASN D 43 GLN E 200 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.076156 restraints weight = 10027.181| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.18 r_work: 0.2769 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6735 Z= 0.122 Angle : 0.533 9.611 9194 Z= 0.262 Chirality : 0.044 0.212 1064 Planarity : 0.004 0.033 1172 Dihedral : 8.697 62.449 1080 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 13.06 % Favored : 84.41 % 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: -0.22 (0.28), residues: 819 helix: -2.52 (0.51), residues: 72 sheet: 0.61 (0.36), residues: 205 loop : -0.03 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 272 TYR 0.020 0.001 TYR B 31 PHE 0.013 0.001 PHE A 100 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6728) covalent geometry : angle 0.52515 / 0.26 ( 9173) hydrogen bonds : bond 0.03595 / 2.33 ( 174) hydrogen bonds : angle 6.29529 / 4.34 ( 510) glycosidic custom : bond 0.00142 / 0.07 ( 1) glycosidic custom : angle 1.15887 / 0.49 ( 3) link_ALPHA1-3 : bond 0.00644 / 0.34 ( 1) link_ALPHA1-3 : angle 2.65979 / 1.27 ( 3) link_ALPHA1-6 : bond 0.00614 / 0.32 ( 1) link_ALPHA1-6 : angle 1.49357 / 0.82 ( 3) link_BETA1-4 : bond 0.00635 / 0.24 ( 3) link_BETA1-4 : angle 2.33014 / 1.08 ( 9) link_BETA1-6 : bond 0.00540 / 0.28 ( 1) link_BETA1-6 : angle 1.03474 / 0.44 ( 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 118 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.213 Fit side-chains REVERT: A 272 ARG cc_start: 0.8253 (mtm110) cc_final: 0.8019 (mtm110) REVERT: B 27 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: B 52 LYS cc_start: 0.9325 (tttm) cc_final: 0.7249 (mppt) REVERT: B 102 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 111 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8768 (mp-120) REVERT: C 220 ASP cc_start: 0.8513 (p0) cc_final: 0.8032 (p0) outliers start: 18 outliers final: 8 residues processed: 115 average time/residue: 0.4912 time to fit residues: 59.6815 Evaluate side-chains 104 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 43 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [42, 47, 16, 8, 56, 68, 14, 12, 19, 21, 43] chunk 42 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 160 GLN D 43 GLN E 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.091729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.074434 restraints weight = 10040.873| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.19 r_work: 0.2740 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6735 Z= 0.182 Angle : 0.546 8.958 9194 Z= 0.271 Chirality : 0.044 0.232 1064 Planarity : 0.004 0.029 1172 Dihedral : 6.883 57.587 1078 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.09 % Allowed : 12.92 % Favored : 83.99 % 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: -2.25 (0.54), residues: 70 sheet: 0.65 (0.36), residues: 205 loop : -0.06 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.023 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS B 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 6728) covalent geometry : angle 0.53690 / 0.27 ( 9173) hydrogen bonds : bond 0.03713 / 2.43 ( 174) hydrogen bonds : angle 5.96955 / 4.12 ( 510) glycosidic custom : bond 0.00050 / 0.03 ( 1) glycosidic custom : angle 1.17091 / 0.48 ( 3) link_ALPHA1-3 : bond 0.00160 / 0.08 ( 1) link_ALPHA1-3 : angle 3.25720 / 1.59 ( 3) link_ALPHA1-6 : bond 0.00525 / 0.28 ( 1) link_ALPHA1-6 : angle 1.49518 / 0.83 ( 3) link_BETA1-4 : bond 0.00621 / 0.24 ( 3) link_BETA1-4 : angle 2.36826 / 1.11 ( 9) link_BETA1-6 : bond 0.00525 / 0.28 ( 1) link_BETA1-6 : angle 1.02909 / 0.43 ( 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 118 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.253 Fit side-chains REVERT: A 2 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: B 52 LYS cc_start: 0.9355 (tttm) cc_final: 0.7232 (mppt) REVERT: B 102 TYR cc_start: 0.9413 (OUTLIER) cc_final: 0.8686 (t80) REVERT: B 111 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8781 (mp-120) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.4920 time to fit residues: 57.6241 Evaluate side-chains 110 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain D residue 43 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [78, 52, 7, 5, 24, 64, 15, 68, 19, 46, 43] chunk 78 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 ASN D 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.072700 restraints weight = 10175.460| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.19 r_work: 0.2708 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6735 Z= 0.251 Angle : 0.576 8.854 9194 Z= 0.288 Chirality : 0.046 0.243 1064 Planarity : 0.004 0.033 1172 Dihedral : 6.750 54.934 1078 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.09 % Allowed : 12.78 % Favored : 84.13 % 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: -0.26 (0.28), residues: 819 helix: -2.23 (0.53), residues: 71 sheet: 0.60 (0.36), residues: 205 loop : -0.13 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 272 TYR 0.025 0.002 TYR B 31 PHE 0.013 0.002 PHE C 222 TRP 0.008 0.001 TRP A 249 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 ( 6728) covalent geometry : angle 0.56731 / 0.29 ( 9173) hydrogen bonds : bond 0.03821 / 2.53 ( 174) hydrogen bonds : angle 5.91850 / 4.07 ( 510) glycosidic custom : bond 0.00196 / 0.10 ( 1) glycosidic custom : angle 1.27330 / 0.53 ( 3) link_ALPHA1-3 : bond 0.00014 / 0.01 ( 1) link_ALPHA1-3 : angle 3.49374 / 1.64 ( 3) link_ALPHA1-6 : bond 0.00555 / 0.29 ( 1) link_ALPHA1-6 : angle 1.60614 / 0.90 ( 3) link_BETA1-4 : bond 0.00611 / 0.24 ( 3) link_BETA1-4 : angle 2.30290 / 1.06 ( 9) link_BETA1-6 : bond 0.00494 / 0.26 ( 1) link_BETA1-6 : angle 1.01817 / 0.41 ( 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 117 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.179 Fit side-chains REVERT: A 2 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: A 272 ARG cc_start: 0.8356 (mtm110) cc_final: 0.8134 (mtm110) REVERT: B 52 LYS cc_start: 0.9389 (tttm) cc_final: 0.7232 (mppt) REVERT: B 72 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8480 (mm-30) REVERT: B 102 TYR cc_start: 0.9454 (OUTLIER) cc_final: 0.8704 (t80) REVERT: B 111 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8781 (mp-120) REVERT: B 151 GLU cc_start: 0.8240 (pm20) cc_final: 0.8018 (pm20) REVERT: C 145 GLU cc_start: 0.8625 (pm20) cc_final: 0.8423 (pm20) outliers start: 22 outliers final: 10 residues processed: 110 average time/residue: 0.4964 time to fit residues: 57.6263 Evaluate side-chains 106 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 46 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [48, 0, 59, 74, 40, 16, 12, 3, 67, 37, 47] chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.073477 restraints weight = 10147.288| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.17 r_work: 0.2724 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6735 Z= 0.186 Angle : 0.545 9.074 9194 Z= 0.271 Chirality : 0.044 0.247 1064 Planarity : 0.004 0.032 1172 Dihedral : 6.588 54.706 1078 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.37 % Allowed : 12.36 % Favored : 84.27 % 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: -0.25 (0.28), residues: 819 helix: -2.13 (0.55), residues: 70 sheet: 0.56 (0.36), residues: 205 loop : -0.12 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 272 TYR 0.024 0.001 TYR B 31 PHE 0.012 0.001 PHE C 215 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 ( 6728) covalent geometry : angle 0.53624 / 0.27 ( 9173) hydrogen bonds : bond 0.03528 / 2.33 ( 174) hydrogen bonds : angle 5.79162 / 3.98 ( 510) glycosidic custom : bond 0.00050 / 0.03 ( 1) glycosidic custom : angle 1.14554 / 0.48 ( 3) link_ALPHA1-3 : bond 0.00149 / 0.08 ( 1) link_ALPHA1-3 : angle 3.46936 / 1.62 ( 3) link_ALPHA1-6 : bond 0.00468 / 0.25 ( 1) link_ALPHA1-6 : angle 1.64898 / 0.92 ( 3) link_BETA1-4 : bond 0.00608 / 0.23 ( 3) link_BETA1-4 : angle 2.15633 / 0.99 ( 9) link_BETA1-6 : bond 0.00481 / 0.25 ( 1) link_BETA1-6 : angle 1.03907 / 0.42 ( 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 116 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.251 Fit side-chains REVERT: A 272 ARG cc_start: 0.8376 (mtm110) cc_final: 0.8153 (mtm110) REVERT: B 52 LYS cc_start: 0.9387 (tttm) cc_final: 0.7247 (mppt) REVERT: B 72 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8466 (mm-30) REVERT: B 102 TYR cc_start: 0.9461 (OUTLIER) cc_final: 0.8507 (t80) REVERT: B 111 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8771 (mp-120) outliers start: 24 outliers final: 11 residues processed: 108 average time/residue: 0.4883 time to fit residues: 55.7501 Evaluate side-chains 108 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 46 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [7, 4, 48, 30, 17, 45, 36, 37, 0, 55, 49] chunk 7 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.1980 chunk 45 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.074769 restraints weight = 10139.092| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.20 r_work: 0.2743 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6735 Z= 0.142 Angle : 0.534 9.166 9194 Z= 0.265 Chirality : 0.044 0.236 1064 Planarity : 0.004 0.033 1172 Dihedral : 6.382 54.721 1078 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.95 % Allowed : 12.08 % Favored : 84.97 % 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: -0.24 (0.28), residues: 819 helix: -2.03 (0.56), residues: 69 sheet: 0.59 (0.37), residues: 195 loop : -0.13 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.023 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.007 0.001 TRP A 249 HIS 0.003 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 6728) covalent geometry : angle 0.52512 / 0.26 ( 9173) hydrogen bonds : bond 0.03259 / 2.15 ( 174) hydrogen bonds : angle 5.62700 / 3.87 ( 510) glycosidic custom : bond 0.00126 / 0.07 ( 1) glycosidic custom : angle 1.16721 / 0.50 ( 3) link_ALPHA1-3 : bond 0.00123 / 0.06 ( 1) link_ALPHA1-3 : angle 3.46240 / 1.62 ( 3) link_ALPHA1-6 : bond 0.00454 / 0.24 ( 1) link_ALPHA1-6 : angle 1.68380 / 0.93 ( 3) link_BETA1-4 : bond 0.00645 / 0.24 ( 3) link_BETA1-4 : angle 2.09096 / 0.96 ( 9) link_BETA1-6 : bond 0.00527 / 0.28 ( 1) link_BETA1-6 : angle 1.04566 / 0.42 ( 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 115 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.216 Fit side-chains REVERT: A 82 SER cc_start: 0.6140 (OUTLIER) cc_final: 0.5862 (t) REVERT: B 52 LYS cc_start: 0.9355 (tttm) cc_final: 0.7240 (mppt) REVERT: B 72 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8455 (mm-30) REVERT: B 111 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8771 (mp-120) REVERT: C 153 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9054 (tp) outliers start: 21 outliers final: 11 residues processed: 109 average time/residue: 0.5230 time to fit residues: 60.1171 Evaluate side-chains 107 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain D residue 46 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [25, 14, 78, 75, 41, 46, 22, 64, 44, 74, 77] chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 0.0070 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.093007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.075844 restraints weight = 9954.587| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.18 r_work: 0.2763 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6735 Z= 0.115 Angle : 0.515 9.406 9194 Z= 0.254 Chirality : 0.043 0.222 1064 Planarity : 0.004 0.034 1172 Dihedral : 6.189 54.660 1078 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.81 % Allowed : 12.64 % Favored : 84.55 % 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: -1.92 (0.56), residues: 70 sheet: 0.59 (0.37), residues: 195 loop : -0.11 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.023 0.001 TYR B 31 PHE 0.010 0.001 PHE C 215 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS B 175 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 6728) covalent geometry : angle 0.50596 / 0.25 ( 9173) hydrogen bonds : bond 0.03005 / 1.96 ( 174) hydrogen bonds : angle 5.35265 / 3.70 ( 510) glycosidic custom : bond 0.00187 / 0.10 ( 1) glycosidic custom : angle 1.13650 / 0.49 ( 3) link_ALPHA1-3 : bond 0.00179 / 0.09 ( 1) link_ALPHA1-3 : angle 3.44126 / 1.62 ( 3) link_ALPHA1-6 : bond 0.00507 / 0.27 ( 1) link_ALPHA1-6 : angle 1.66746 / 0.92 ( 3) link_BETA1-4 : bond 0.00629 / 0.24 ( 3) link_BETA1-4 : angle 2.01266 / 0.93 ( 9) link_BETA1-6 : bond 0.00563 / 0.30 ( 1) link_BETA1-6 : angle 1.02556 / 0.43 ( 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 113 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.273 Fit side-chains REVERT: A 82 SER cc_start: 0.6263 (OUTLIER) cc_final: 0.5969 (t) REVERT: B 52 LYS cc_start: 0.9325 (tttm) cc_final: 0.7144 (mppt) REVERT: B 72 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8458 (mm-30) REVERT: B 151 GLU cc_start: 0.8165 (pm20) cc_final: 0.7963 (pm20) REVERT: C 153 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9055 (tp) REVERT: C 220 ASP cc_start: 0.8521 (p0) cc_final: 0.8149 (p0) outliers start: 20 outliers final: 12 residues processed: 108 average time/residue: 0.5099 time to fit residues: 58.2272 Evaluate side-chains 107 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 0, 3, 15, 63, 21, 45, 14, 67, 48, 16] chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 21 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 228 HIS B 240 ASN D 30 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.074153 restraints weight = 10022.512| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.17 r_work: 0.2736 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6735 Z= 0.187 Angle : 0.545 9.058 9194 Z= 0.270 Chirality : 0.044 0.237 1064 Planarity : 0.004 0.034 1172 Dihedral : 6.190 54.326 1078 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.67 % Allowed : 13.34 % Favored : 83.99 % 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: -1.95 (0.55), residues: 70 sheet: 0.63 (0.37), residues: 195 loop : -0.14 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.025 0.001 TYR B 31 PHE 0.012 0.001 PHE C 222 TRP 0.006 0.001 TRP A 249 HIS 0.004 0.001 HIS A 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 ( 6728) covalent geometry : angle 0.53646 / 0.27 ( 9173) hydrogen bonds : bond 0.03298 / 2.15 ( 174) hydrogen bonds : angle 5.42372 / 3.75 ( 510) glycosidic custom : bond 0.00126 / 0.07 ( 1) glycosidic custom : angle 1.31555 / 0.56 ( 3) link_ALPHA1-3 : bond 0.00098 / 0.05 ( 1) link_ALPHA1-3 : angle 3.42491 / 1.60 ( 3) link_ALPHA1-6 : bond 0.00487 / 0.26 ( 1) link_ALPHA1-6 : angle 1.66448 / 0.92 ( 3) link_BETA1-4 : bond 0.00609 / 0.23 ( 3) link_BETA1-4 : angle 1.99064 / 0.90 ( 9) link_BETA1-6 : bond 0.00539 / 0.28 ( 1) link_BETA1-6 : angle 1.00821 / 0.42 ( 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 111 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.283 Fit side-chains REVERT: A 2 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: A 82 SER cc_start: 0.6173 (OUTLIER) cc_final: 0.5866 (t) REVERT: B 52 LYS cc_start: 0.9346 (tttm) cc_final: 0.7222 (mppt) REVERT: B 72 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8459 (mm-30) REVERT: C 153 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9043 (tp) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.5055 time to fit residues: 56.5492 Evaluate side-chains 108 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [17, 56, 39, 60, 9, 16, 63, 6, 36, 0, 66] chunk 17 optimal weight: 0.0770 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.074732 restraints weight = 10070.434| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.19 r_work: 0.2745 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6735 Z= 0.155 Angle : 0.547 9.013 9194 Z= 0.272 Chirality : 0.044 0.239 1064 Planarity : 0.004 0.034 1172 Dihedral : 6.156 54.327 1078 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.53 % Allowed : 13.76 % Favored : 83.71 % 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: -0.24 (0.28), residues: 819 helix: -1.92 (0.55), residues: 70 sheet: 0.60 (0.37), residues: 195 loop : -0.15 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 104 TYR 0.023 0.001 TYR B 31 PHE 0.011 0.001 PHE C 222 TRP 0.006 0.001 TRP A 249 HIS 0.002 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6728) covalent geometry : angle 0.53921 / 0.27 ( 9173) hydrogen bonds : bond 0.03157 / 2.06 ( 174) hydrogen bonds : angle 5.37468 / 3.72 ( 510) glycosidic custom : bond 0.00103 / 0.05 ( 1) glycosidic custom : angle 1.19590 / 0.51 ( 3) link_ALPHA1-3 : bond 0.00205 / 0.11 ( 1) link_ALPHA1-3 : angle 3.37973 / 1.59 ( 3) link_ALPHA1-6 : bond 0.00499 / 0.26 ( 1) link_ALPHA1-6 : angle 1.64957 / 0.91 ( 3) link_BETA1-4 : bond 0.00636 / 0.24 ( 3) link_BETA1-4 : angle 1.97238 / 0.90 ( 9) link_BETA1-6 : bond 0.00546 / 0.29 ( 1) link_BETA1-6 : angle 1.02819 / 0.43 ( 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 112 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.177 Fit side-chains REVERT: A 2 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: A 82 SER cc_start: 0.6128 (OUTLIER) cc_final: 0.5874 (t) REVERT: B 52 LYS cc_start: 0.9345 (tttm) cc_final: 0.7215 (mppt) REVERT: B 72 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8446 (mm-30) REVERT: C 153 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9051 (tp) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.5038 time to fit residues: 56.8314 Evaluate side-chains 110 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [37, 22, 60, 72, 64, 28, 76, 63, 46, 65, 75] chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 46 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.073381 restraints weight = 10064.247| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.17 r_work: 0.2722 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6735 Z= 0.217 Angle : 0.571 9.393 9194 Z= 0.284 Chirality : 0.045 0.251 1064 Planarity : 0.004 0.034 1172 Dihedral : 6.220 54.029 1078 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.53 % Allowed : 14.04 % Favored : 83.43 % 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: -0.29 (0.28), residues: 819 helix: -1.96 (0.54), residues: 70 sheet: 0.59 (0.37), residues: 195 loop : -0.19 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.026 0.002 TYR B 31 PHE 0.014 0.001 PHE C 222 TRP 0.007 0.001 TRP C 109 HIS 0.003 0.001 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 ( 6728) covalent geometry : angle 0.56333 / 0.28 ( 9173) hydrogen bonds : bond 0.03431 / 2.24 ( 174) hydrogen bonds : angle 5.48482 / 3.80 ( 510) glycosidic custom : bond 0.00087 / 0.05 ( 1) glycosidic custom : angle 1.28229 / 0.54 ( 3) link_ALPHA1-3 : bond 0.00189 / 0.10 ( 1) link_ALPHA1-3 : angle 3.35119 / 1.57 ( 3) link_ALPHA1-6 : bond 0.00474 / 0.25 ( 1) link_ALPHA1-6 : angle 1.66222 / 0.93 ( 3) link_BETA1-4 : bond 0.00629 / 0.24 ( 3) link_BETA1-4 : angle 1.96611 / 0.89 ( 9) link_BETA1-6 : bond 0.00526 / 0.28 ( 1) link_BETA1-6 : angle 1.00773 / 0.42 ( 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 113 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.343 Fit side-chains REVERT: A 82 SER cc_start: 0.6125 (OUTLIER) cc_final: 0.5882 (t) REVERT: B 52 LYS cc_start: 0.9368 (tttm) cc_final: 0.7227 (mppt) REVERT: B 72 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8444 (mm-30) REVERT: B 151 GLU cc_start: 0.8213 (pm20) cc_final: 0.8010 (pm20) REVERT: C 220 ASP cc_start: 0.8641 (p0) cc_final: 0.8211 (p0) outliers start: 18 outliers final: 12 residues processed: 108 average time/residue: 0.5099 time to fit residues: 58.1093 Evaluate side-chains 109 residues out of total 712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [26, 38, 39, 55, 32, 31, 54, 27, 47, 50, 48] chunk 26 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 240 ASN D 30 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078291 restraints weight = 10548.720| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.05 r_work: 0.2847 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6735 Z= 0.096 Angle : 0.520 9.411 9194 Z= 0.257 Chirality : 0.042 0.220 1064 Planarity : 0.004 0.034 1172 Dihedral : 5.985 54.391 1078 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.69 % Allowed : 14.61 % Favored : 83.71 % 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: -0.24 (0.28), residues: 819 helix: -1.85 (0.56), residues: 70 sheet: 0.56 (0.37), residues: 195 loop : -0.15 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 104 TYR 0.020 0.001 TYR B 31 PHE 0.009 0.001 PHE A 100 TRP 0.007 0.001 TRP B 207 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 ( 6728) covalent geometry : angle 0.51166 / 0.26 ( 9173) hydrogen bonds : bond 0.02822 / 1.84 ( 174) hydrogen bonds : angle 5.20627 / 3.61 ( 510) glycosidic custom : bond 0.00486 / 0.26 ( 1) glycosidic custom : angle 1.10169 / 0.50 ( 3) link_ALPHA1-3 : bond 0.00337 / 0.18 ( 1) link_ALPHA1-3 : angle 3.35024 / 1.58 ( 3) link_ALPHA1-6 : bond 0.00488 / 0.26 ( 1) link_ALPHA1-6 : angle 1.61735 / 0.88 ( 3) link_BETA1-4 : bond 0.00725 / 0.28 ( 3) link_BETA1-4 : angle 1.93097 / 0.90 ( 9) link_BETA1-6 : bond 0.00515 / 0.27 ( 1) link_BETA1-6 : angle 1.06648 / 0.44 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2550.65 seconds wall clock time: 44 minutes 19.37 seconds (2659.37 seconds total)