Starting phenix.real_space_refine on Thu Oct 22 23:24:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.cif Found real_map, /net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.map" model { file = "/net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23ps_69155/10_2026/23ps_69155.cif" } resolution = 2.65 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= 0.039 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 39 5.16 5 C 4172 2.51 5 N 1102 2.21 5 O 1269 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s 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: 6582 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1874 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain: "C" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1908 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: "A" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2312 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 277} Chain breaks: 1 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: 0.87, per 1000 atoms: 0.13 Number of scatterers: 6582 At special positions: 0 Unit cell: (92.169, 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 39 16.00 O 1269 8.00 N 1102 7.00 C 4172 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: 0.32 Conformation dependent library (CDL) restraints added in 188.5 milliseconds 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 12 sheets defined 15.3% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... 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 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 167 through 173 removed outlier: 4.268A pdb=" N THR B 171 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 47 removed outlier: 4.181A pdb=" N VAL C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS C 68 " --> pdb=" O GLN 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 'A' and resid 28 through 32 Processing helix chain 'A' and resid 38 through 43 Processing helix 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 removed outlier: 3.704A pdb=" N LYS A 106 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.550A pdb=" N TRP A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLN A 163 " --> pdb=" O PHE A 160 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 164 " --> pdb=" O HIS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 164' Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'E' and resid 201 through 205 Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 18 Processing sheet with id=AA2, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.818A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.818A pdb=" N CYS B 32 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS B 99 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 241 " --> pdb=" O HIS B 99 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 101 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N PHE B 239 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG B 103 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 237 " --> pdb=" O ARG B 103 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 226 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.555A pdb=" N TRP B 207 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 121 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 119 " --> pdb=" O PRO B 216 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 23 removed outlier: 6.415A pdb=" N ALA C 22 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 110 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 249 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 112 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 247 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 114 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 245 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 232 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLU A 75 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 234 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A 73 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A 236 " --> pdb=" O LYS A 71 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS A 71 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 238 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 39 through 40 removed outlier: 4.277A pdb=" N ALA A 247 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 245 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG A 114 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ALA A 247 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR A 112 " --> pdb=" O ALA A 247 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 249 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE A 110 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA8, first strand: chain 'C' and resid 51 through 52 Processing sheet with id=AA9, first strand: chain 'C' and resid 80 through 85 removed outlier: 6.898A pdb=" N CYS C 194 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASN C 83 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 192 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS C 128 " --> pdb=" O GLN C 197 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN C 199 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR C 126 " --> pdb=" O ASN C 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 176 through 177 removed outlier: 6.276A pdb=" N TYR C 106 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET C 227 " --> pdb=" O TYR C 106 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB3, first strand: chain 'A' and resid 90 through 94 removed outlier: 4.137A pdb=" N ALA A 168 " --> pdb=" O PHE A 146 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 477 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: 0.49 Time building geometry restraints manager: 0.41 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: 2118 1.34 - 1.46: 1211 1.46 - 1.57: 3349 1.57 - 1.69: 1 1.69 - 1.81: 64 Bond restraints: 6743 Sorted by residual: bond pdb=" CA ASN A 211 " pdb=" C ASN A 211 " ideal model delta sigma weight residual 1.523 1.491 0.032 1.31e-02 5.83e+03 5.85e+00 bond pdb=" N ASN A 211 " pdb=" CA ASN A 211 " ideal model delta sigma weight residual 1.460 1.439 0.021 1.10e-02 8.26e+03 3.50e+00 bond pdb=" CA CYS A 220 " pdb=" C CYS A 220 " ideal model delta sigma weight residual 1.523 1.503 0.019 1.23e-02 6.61e+03 2.49e+00 bond pdb=" C ASN A 211 " pdb=" O ASN A 211 " ideal model delta sigma weight residual 1.241 1.223 0.018 1.14e-02 7.69e+03 2.46e+00 bond pdb=" CA THR A 215 " pdb=" C THR A 215 " ideal model delta sigma weight residual 1.525 1.506 0.019 1.25e-02 6.40e+03 2.25e+00 ... (remaining 6738 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 9008 1.67 - 3.34: 154 3.34 - 5.00: 22 5.00 - 6.67: 5 6.67 - 8.34: 1 Bond angle restraints: 9190 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 112.60 118.01 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" CA GLU B 74 " pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " ideal model delta sigma weight residual 114.10 120.00 -5.90 2.00e+00 2.50e-01 8.72e+00 angle pdb=" CA GLU A 19 " pdb=" CB GLU A 19 " pdb=" CG GLU A 19 " ideal model delta sigma weight residual 114.10 119.71 -5.61 2.00e+00 2.50e-01 7.86e+00 angle pdb=" C CYS A 220 " pdb=" N VAL A 221 " pdb=" CA VAL A 221 " ideal model delta sigma weight residual 123.14 119.57 3.57 1.31e+00 5.83e-01 7.42e+00 angle pdb=" CB GLU B 74 " pdb=" CG GLU B 74 " pdb=" CD GLU B 74 " ideal model delta sigma weight residual 112.60 117.18 -4.58 1.70e+00 3.46e-01 7.26e+00 ... (remaining 9185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 3773 21.87 - 43.75: 273 43.75 - 65.62: 63 65.62 - 87.49: 18 87.49 - 109.36: 8 Dihedral angle restraints: 4135 sinusoidal: 1731 harmonic: 2404 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 -54.61 109.36 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 67.47 108.66 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 -66.66 -107.87 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 4132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 833 0.047 - 0.094: 173 0.094 - 0.141: 57 0.141 - 0.188: 1 0.188 - 0.235: 2 Chirality restraints: 1066 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 9.00e+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 0.24 2.00e-01 2.50e+01 1.38e+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 -2.39 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1063 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 209 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C GLY A 209 " 0.029 2.00e-02 2.50e+03 pdb=" O GLY A 209 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 210 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 59 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" CD GLU C 59 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLU C 59 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU C 59 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 12 " 0.102 9.50e-02 1.11e+02 4.58e-02 1.58e+00 pdb=" NE ARG B 12 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 12 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 12 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 12 " 0.001 2.00e-02 2.50e+03 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 1.21 - 1.95: 4 1.95 - 2.69: 107 2.69 - 3.43: 8901 3.43 - 4.16: 16782 4.16 - 4.90: 29346 Nonbonded interactions: 55140 Sorted by model distance: nonbonded pdb=" CB ALA A 200 " pdb=" CD ARG E 205 " model vdw 1.214 3.860 nonbonded pdb=" CD2 LEU A 207 " pdb=" O ARG E 205 " model vdw 1.644 3.460 nonbonded pdb=" CB ALA A 200 " pdb=" NE ARG E 205 " model vdw 1.785 3.540 nonbonded pdb=" CD2 LEU A 207 " pdb=" C ARG E 205 " model vdw 1.912 3.690 nonbonded pdb=" OG1 THR A 94 " pdb=" OD1 ASN E 200 " model vdw 1.958 3.040 ... (remaining 55135 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 : 0.004 0.037 6750 Z= 0.186 Angle : 0.555 8.342 9211 Z= 0.285 Chirality : 0.043 0.235 1066 Planarity : 0.004 0.046 1172 Dihedral : 17.177 109.364 2579 Min Nonbonded Distance : 1.214 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.11 % Allowed : 19.08 % Favored : 79.81 % 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: 0.02 (0.28), residues: 816 helix: -2.36 (0.55), residues: 65 sheet: 0.70 (0.35), residues: 210 loop : 0.12 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 12 TYR 0.011 0.001 TYR B 31 PHE 0.007 0.001 PHE B 200 TRP 0.004 0.001 TRP A 248 HIS 0.002 0.000 HIS C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.19 ( 6743) covalent geometry : angle 0.54586 / 0.28 ( 9190) hydrogen bonds : bond 0.18799 / 12.42 ( 171) hydrogen bonds : angle 9.29359 / 6.38 ( 477) glycosidic custom : bond 0.00000 / 0.00 ( 1) glycosidic custom : angle 0.61364 / 0.32 ( 3) link_ALPHA1-3 : bond 0.00391 / 0.21 ( 1) link_ALPHA1-3 : angle 3.53161 / 1.84 ( 3) link_ALPHA1-6 : bond 0.00769 / 0.40 ( 1) link_ALPHA1-6 : angle 1.48437 / 0.84 ( 3) link_BETA1-4 : bond 0.00675 / 0.34 ( 3) link_BETA1-4 : angle 2.41055 / 1.33 ( 9) link_BETA1-6 : bond 0.00552 / 0.29 ( 1) link_BETA1-6 : angle 1.07165 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: B 52 LYS cc_start: 0.9444 (tttm) cc_final: 0.6996 (mppt) REVERT: B 150 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7985 (mp0) REVERT: C 52 MET cc_start: 0.9456 (mtm) cc_final: 0.9027 (mtm) REVERT: C 79 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8606 (mp10) REVERT: A 13 LYS cc_start: 0.8881 (pttt) cc_final: 0.8617 (ptmm) REVERT: A 41 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8908 (mt-10) REVERT: A 78 ASN cc_start: 0.7276 (p0) cc_final: 0.6584 (t0) REVERT: A 135 MET cc_start: 0.4130 (ttt) cc_final: 0.2762 (mpp) REVERT: A 218 ASN cc_start: 0.7666 (m-40) cc_final: 0.7463 (m110) REVERT: A 246 LYS cc_start: 0.8890 (mttp) cc_final: 0.8583 (mtpt) outliers start: 8 outliers final: 2 residues processed: 137 average time/residue: 0.3774 time to fit residues: 54.2779 Evaluate side-chains 110 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU 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: 10.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN B 30 ASN B 45 HIS B 55 GLN B 206 GLN C 60 ASN C 65 GLN C 160 GLN C 240 HIS C 247 GLN D 43 GLN A 131 ASN A 228 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.095778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.079961 restraints weight = 10990.848| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.16 r_work: 0.2760 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 6750 Z= 0.319 Angle : 0.631 7.917 9211 Z= 0.317 Chirality : 0.048 0.240 1066 Planarity : 0.005 0.046 1172 Dihedral : 8.239 59.608 1074 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.79 % Allowed : 17.41 % Favored : 79.81 % 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: -0.12 (0.28), residues: 816 helix: -2.08 (0.54), residues: 68 sheet: 0.72 (0.36), residues: 197 loop : -0.05 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 205 TYR 0.010 0.002 TYR A 192 PHE 0.016 0.002 PHE C 215 TRP 0.007 0.001 TRP A 248 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.32 ( 6743) covalent geometry : angle 0.62384 / 0.32 ( 9190) hydrogen bonds : bond 0.04235 / 2.81 ( 171) hydrogen bonds : angle 6.80678 / 4.62 ( 477) glycosidic custom : bond 0.00150 / 0.08 ( 1) glycosidic custom : angle 1.32488 / 0.70 ( 3) link_ALPHA1-3 : bond 0.00193 / 0.10 ( 1) link_ALPHA1-3 : angle 2.98168 / 1.57 ( 3) link_ALPHA1-6 : bond 0.00483 / 0.25 ( 1) link_ALPHA1-6 : angle 1.65679 / 0.94 ( 3) link_BETA1-4 : bond 0.00382 / 0.19 ( 3) link_BETA1-4 : angle 2.13228 / 1.19 ( 9) link_BETA1-6 : bond 0.00231 / 0.12 ( 1) link_BETA1-6 : angle 1.60816 / 0.82 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.262 Fit side-chains REVERT: B 52 LYS cc_start: 0.9480 (tttm) cc_final: 0.7201 (mppt) REVERT: C 59 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 79 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8777 (mp10) REVERT: C 148 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8831 (ppp) REVERT: C 220 ASP cc_start: 0.8869 (p0) cc_final: 0.8506 (p0) REVERT: A 41 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8901 (mt-10) REVERT: A 78 ASN cc_start: 0.7417 (p0) cc_final: 0.6782 (t0) REVERT: A 246 LYS cc_start: 0.9003 (mttp) cc_final: 0.8766 (mttm) REVERT: A 284 GLU cc_start: 0.8800 (tp30) cc_final: 0.8381 (tp30) outliers start: 20 outliers final: 6 residues processed: 123 average time/residue: 0.5903 time to fit residues: 76.0117 Evaluate side-chains 108 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [32, 45, 64, 1, 66, 8, 53, 14, 73, 58, 9] chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.095112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.079225 restraints weight = 10700.581| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.15 r_work: 0.2805 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6750 Z= 0.121 Angle : 0.522 8.360 9211 Z= 0.262 Chirality : 0.042 0.203 1066 Planarity : 0.004 0.035 1172 Dihedral : 6.625 57.158 1074 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.65 % Allowed : 15.32 % Favored : 82.03 % 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: -0.02 (0.28), residues: 816 helix: -1.79 (0.59), residues: 66 sheet: 0.76 (0.36), residues: 197 loop : -0.01 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 12 TYR 0.010 0.001 TYR B 31 PHE 0.009 0.001 PHE C 215 TRP 0.006 0.001 TRP A 248 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 6743) covalent geometry : angle 0.51233 / 0.26 ( 9190) hydrogen bonds : bond 0.03379 / 2.20 ( 171) hydrogen bonds : angle 6.30150 / 4.29 ( 477) glycosidic custom : bond 0.00223 / 0.12 ( 1) glycosidic custom : angle 1.06936 / 0.56 ( 3) link_ALPHA1-3 : bond 0.00030 / 0.02 ( 1) link_ALPHA1-3 : angle 3.38034 / 1.79 ( 3) link_ALPHA1-6 : bond 0.00609 / 0.32 ( 1) link_ALPHA1-6 : angle 1.56444 / 0.89 ( 3) link_BETA1-4 : bond 0.00546 / 0.27 ( 3) link_BETA1-4 : angle 2.21501 / 1.25 ( 9) link_BETA1-6 : bond 0.00370 / 0.19 ( 1) link_BETA1-6 : angle 1.30560 / 0.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.250 Fit side-chains REVERT: B 52 LYS cc_start: 0.9451 (tttm) cc_final: 0.7244 (mppt) REVERT: C 79 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8745 (mp10) REVERT: C 148 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8813 (ppp) REVERT: A 41 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8876 (mt-10) REVERT: A 78 ASN cc_start: 0.7439 (p0) cc_final: 0.6773 (t0) REVERT: A 92 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8891 (tmtt) REVERT: A 246 LYS cc_start: 0.8965 (mttp) cc_final: 0.8660 (mtpt) REVERT: A 284 GLU cc_start: 0.8769 (tp30) cc_final: 0.8271 (tp30) outliers start: 19 outliers final: 6 residues processed: 123 average time/residue: 0.5804 time to fit residues: 74.7637 Evaluate side-chains 115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [27, 26, 70, 23, 16, 73, 37, 18, 36, 78, 7] chunk 27 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 206 GLN C 101 ASN C 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.092473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.076506 restraints weight = 10928.432| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.15 r_work: 0.2763 rms_B_bonded: 2.32 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: 0.8836 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6750 Z= 0.231 Angle : 0.550 8.105 9211 Z= 0.277 Chirality : 0.045 0.226 1066 Planarity : 0.004 0.043 1172 Dihedral : 6.403 57.793 1074 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.65 % Allowed : 15.88 % Favored : 81.48 % 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: -0.14 (0.27), residues: 816 helix: -1.82 (0.58), residues: 69 sheet: 0.71 (0.36), residues: 197 loop : -0.11 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 271 TYR 0.033 0.002 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.23 ( 6743) covalent geometry : angle 0.54134 / 0.27 ( 9190) hydrogen bonds : bond 0.03571 / 2.35 ( 171) hydrogen bonds : angle 6.15067 / 4.20 ( 477) glycosidic custom : bond 0.00158 / 0.08 ( 1) glycosidic custom : angle 1.22421 / 0.65 ( 3) link_ALPHA1-3 : bond 0.00222 / 0.12 ( 1) link_ALPHA1-3 : angle 3.72997 / 1.95 ( 3) link_ALPHA1-6 : bond 0.00477 / 0.25 ( 1) link_ALPHA1-6 : angle 1.67906 / 0.95 ( 3) link_BETA1-4 : bond 0.00466 / 0.23 ( 3) link_BETA1-4 : angle 1.97464 / 1.11 ( 9) link_BETA1-6 : bond 0.00243 / 0.13 ( 1) link_BETA1-6 : angle 1.46824 / 0.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.152 Fit side-chains REVERT: B 52 LYS cc_start: 0.9473 (tttm) cc_final: 0.7251 (mppt) REVERT: C 79 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8809 (mp10) REVERT: C 148 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8867 (ppp) REVERT: A 41 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8943 (mt-10) REVERT: A 78 ASN cc_start: 0.7604 (p0) cc_final: 0.6913 (t0) REVERT: A 246 LYS cc_start: 0.8996 (mttp) cc_final: 0.8713 (mttt) outliers start: 19 outliers final: 7 residues processed: 118 average time/residue: 0.5891 time to fit residues: 72.6614 Evaluate side-chains 110 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [61, 27, 2, 59, 33, 60, 31, 38, 36, 22, 6] chunk 61 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN B 240 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.079606 restraints weight = 10822.393| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.17 r_work: 0.2813 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6750 Z= 0.104 Angle : 0.501 8.603 9211 Z= 0.249 Chirality : 0.042 0.206 1066 Planarity : 0.004 0.038 1172 Dihedral : 6.049 54.913 1074 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.81 % Allowed : 16.99 % Favored : 81.20 % 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: 816 helix: -1.81 (0.58), residues: 69 sheet: 0.71 (0.35), residues: 198 loop : -0.07 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 271 TYR 0.009 0.001 TYR A 192 PHE 0.007 0.001 PHE C 215 TRP 0.006 0.001 TRP A 248 HIS 0.002 0.000 HIS C 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6743) covalent geometry : angle 0.49159 / 0.25 ( 9190) hydrogen bonds : bond 0.02920 / 1.90 ( 171) hydrogen bonds : angle 5.76814 / 3.94 ( 477) glycosidic custom : bond 0.00449 / 0.24 ( 1) glycosidic custom : angle 1.14640 / 0.61 ( 3) link_ALPHA1-3 : bond 0.00121 / 0.06 ( 1) link_ALPHA1-3 : angle 3.51878 / 1.84 ( 3) link_ALPHA1-6 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-6 : angle 1.61504 / 0.91 ( 3) link_BETA1-4 : bond 0.00632 / 0.32 ( 3) link_BETA1-4 : angle 1.91947 / 1.07 ( 9) link_BETA1-6 : bond 0.00374 / 0.20 ( 1) link_BETA1-6 : angle 1.27218 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.266 Fit side-chains REVERT: B 52 LYS cc_start: 0.9433 (tttm) cc_final: 0.7305 (mppt) REVERT: B 150 GLU cc_start: 0.8570 (pm20) cc_final: 0.8265 (pm20) REVERT: C 79 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8728 (mp10) REVERT: C 148 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8809 (ppp) REVERT: A 41 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8951 (mt-10) REVERT: A 78 ASN cc_start: 0.7519 (p0) cc_final: 0.6876 (t0) REVERT: A 246 LYS cc_start: 0.8979 (mttp) cc_final: 0.8676 (mtpt) outliers start: 13 outliers final: 7 residues processed: 116 average time/residue: 0.6048 time to fit residues: 73.4243 Evaluate side-chains 113 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [4, 62, 63, 47, 75, 2, 30, 64, 12, 76, 46] chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN B 55 GLN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.077828 restraints weight = 11307.680| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.13 r_work: 0.2769 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 6750 Z= 0.238 Angle : 0.556 9.897 9211 Z= 0.277 Chirality : 0.044 0.226 1066 Planarity : 0.004 0.045 1172 Dihedral : 6.161 56.450 1074 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.53 % Allowed : 17.97 % Favored : 80.50 % 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: -0.14 (0.28), residues: 816 helix: -1.77 (0.58), residues: 69 sheet: 0.71 (0.35), residues: 198 loop : -0.12 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.034 0.002 TYR B 31 PHE 0.013 0.001 PHE C 215 TRP 0.007 0.001 TRP B 177 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 ( 6743) covalent geometry : angle 0.54860 / 0.28 ( 9190) hydrogen bonds : bond 0.03397 / 2.24 ( 171) hydrogen bonds : angle 5.88785 / 4.02 ( 477) glycosidic custom : bond 0.00109 / 0.06 ( 1) glycosidic custom : angle 1.14632 / 0.62 ( 3) link_ALPHA1-3 : bond 0.00140 / 0.07 ( 1) link_ALPHA1-3 : angle 3.62098 / 1.89 ( 3) link_ALPHA1-6 : bond 0.00490 / 0.26 ( 1) link_ALPHA1-6 : angle 1.64840 / 0.93 ( 3) link_BETA1-4 : bond 0.00532 / 0.27 ( 3) link_BETA1-4 : angle 1.77886 / 1.00 ( 9) link_BETA1-6 : bond 0.00229 / 0.12 ( 1) link_BETA1-6 : angle 1.45680 / 0.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.172 Fit side-chains REVERT: B 52 LYS cc_start: 0.9438 (tttm) cc_final: 0.7225 (mppt) REVERT: B 150 GLU cc_start: 0.8652 (pm20) cc_final: 0.8375 (pm20) REVERT: C 79 GLN cc_start: 0.9148 (mm-40) cc_final: 0.8817 (mp10) REVERT: C 148 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8850 (ppp) REVERT: A 41 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8944 (mt-10) REVERT: A 78 ASN cc_start: 0.7580 (p0) cc_final: 0.7006 (t0) REVERT: A 246 LYS cc_start: 0.8996 (mttp) cc_final: 0.8750 (mttm) REVERT: A 284 GLU cc_start: 0.8710 (tp30) cc_final: 0.8256 (tp30) outliers start: 11 outliers final: 9 residues processed: 114 average time/residue: 0.6001 time to fit residues: 71.5060 Evaluate side-chains 112 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [7, 64, 56, 35, 76, 4, 61, 28, 42, 46, 25] chunk 7 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 15 GLN B 55 GLN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.080386 restraints weight = 10856.426| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.15 r_work: 0.2787 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6750 Z= 0.173 Angle : 0.539 10.687 9211 Z= 0.267 Chirality : 0.043 0.218 1066 Planarity : 0.004 0.048 1172 Dihedral : 6.078 55.297 1074 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.09 % Allowed : 17.69 % Favored : 80.22 % 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 (0.28), residues: 816 helix: -1.79 (0.58), residues: 69 sheet: 0.73 (0.35), residues: 197 loop : -0.13 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 271 TYR 0.009 0.001 TYR A 192 PHE 0.010 0.001 PHE C 178 TRP 0.006 0.001 TRP B 177 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 6743) covalent geometry : angle 0.53117 / 0.27 ( 9190) hydrogen bonds : bond 0.03159 / 2.08 ( 171) hydrogen bonds : angle 5.78279 / 3.96 ( 477) glycosidic custom : bond 0.00354 / 0.19 ( 1) glycosidic custom : angle 1.16070 / 0.63 ( 3) link_ALPHA1-3 : bond 0.00034 / 0.02 ( 1) link_ALPHA1-3 : angle 3.57103 / 1.87 ( 3) link_ALPHA1-6 : bond 0.00553 / 0.29 ( 1) link_ALPHA1-6 : angle 1.59768 / 0.90 ( 3) link_BETA1-4 : bond 0.00550 / 0.27 ( 3) link_BETA1-4 : angle 1.74071 / 0.98 ( 9) link_BETA1-6 : bond 0.00249 / 0.13 ( 1) link_BETA1-6 : angle 1.41522 / 0.73 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.232 Fit side-chains REVERT: B 52 LYS cc_start: 0.9415 (tttm) cc_final: 0.7282 (mppt) REVERT: B 150 GLU cc_start: 0.8633 (pm20) cc_final: 0.8344 (pm20) REVERT: C 79 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8781 (mp10) REVERT: C 118 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.9099 (ttp) REVERT: C 148 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8840 (ppp) REVERT: A 41 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8950 (mt-10) REVERT: A 78 ASN cc_start: 0.7561 (p0) cc_final: 0.7087 (t0) REVERT: A 246 LYS cc_start: 0.9017 (mttp) cc_final: 0.8745 (mttt) REVERT: A 284 GLU cc_start: 0.8672 (tp30) cc_final: 0.8226 (tp30) outliers start: 15 outliers final: 10 residues processed: 115 average time/residue: 0.5759 time to fit residues: 69.3324 Evaluate side-chains 115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain E residue 208 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [4, 66, 32, 49, 31, 27, 77, 60, 50, 65, 73] chunk 4 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 0.0970 chunk 65 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN C 96 ASN C 160 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.078945 restraints weight = 10904.362| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.16 r_work: 0.2788 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6750 Z= 0.118 Angle : 0.521 11.383 9211 Z= 0.257 Chirality : 0.042 0.211 1066 Planarity : 0.004 0.050 1172 Dihedral : 5.905 54.682 1074 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.23 % Allowed : 17.27 % Favored : 80.50 % 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: -0.13 (0.28), residues: 816 helix: -1.81 (0.58), residues: 69 sheet: 0.71 (0.35), residues: 198 loop : -0.10 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 271 TYR 0.031 0.001 TYR B 31 PHE 0.008 0.001 PHE C 215 TRP 0.005 0.001 TRP A 248 HIS 0.002 0.000 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 6743) covalent geometry : angle 0.51310 / 0.26 ( 9190) hydrogen bonds : bond 0.02940 / 1.93 ( 171) hydrogen bonds : angle 5.62449 / 3.85 ( 477) glycosidic custom : bond 0.00332 / 0.17 ( 1) glycosidic custom : angle 1.06528 / 0.57 ( 3) link_ALPHA1-3 : bond 0.00128 / 0.07 ( 1) link_ALPHA1-3 : angle 3.49023 / 1.83 ( 3) link_ALPHA1-6 : bond 0.00577 / 0.30 ( 1) link_ALPHA1-6 : angle 1.55912 / 0.88 ( 3) link_BETA1-4 : bond 0.00581 / 0.29 ( 3) link_BETA1-4 : angle 1.72798 / 0.98 ( 9) link_BETA1-6 : bond 0.00300 / 0.16 ( 1) link_BETA1-6 : angle 1.33715 / 0.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.177 Fit side-chains REVERT: B 12 ARG cc_start: 0.8026 (mmm-85) cc_final: 0.7787 (mmm-85) REVERT: B 52 LYS cc_start: 0.9418 (tttm) cc_final: 0.7227 (mppt) REVERT: B 150 GLU cc_start: 0.8599 (pm20) cc_final: 0.8294 (pm20) REVERT: C 79 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8773 (mp10) REVERT: C 118 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.9059 (ttp) REVERT: C 148 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8852 (ppp) REVERT: A 41 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8970 (mt-10) REVERT: A 78 ASN cc_start: 0.7538 (p0) cc_final: 0.7093 (t0) REVERT: A 246 LYS cc_start: 0.9005 (mttp) cc_final: 0.8744 (mttt) REVERT: A 270 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: A 284 GLU cc_start: 0.8682 (tp30) cc_final: 0.8215 (tp30) outliers start: 16 outliers final: 8 residues processed: 117 average time/residue: 0.5943 time to fit residues: 72.8108 Evaluate side-chains 115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 270 GLU 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: [49, 58, 55, 4, 44, 16, 12, 7, 59, 1, 26] chunk 49 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.094751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.079124 restraints weight = 11098.556| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.15 r_work: 0.2765 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6750 Z= 0.246 Angle : 0.588 12.320 9211 Z= 0.292 Chirality : 0.045 0.233 1066 Planarity : 0.004 0.052 1172 Dihedral : 6.109 56.224 1074 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.39 % Allowed : 18.25 % Favored : 80.36 % 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: 816 helix: -1.78 (0.58), residues: 69 sheet: 0.65 (0.36), residues: 198 loop : -0.18 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 271 TYR 0.013 0.002 TYR C 5 PHE 0.013 0.001 PHE C 215 TRP 0.007 0.001 TRP C 109 HIS 0.004 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 ( 6743) covalent geometry : angle 0.58091 / 0.29 ( 9190) hydrogen bonds : bond 0.03494 / 2.31 ( 171) hydrogen bonds : angle 5.84722 / 4.01 ( 477) glycosidic custom : bond 0.00288 / 0.15 ( 1) glycosidic custom : angle 1.22559 / 0.66 ( 3) link_ALPHA1-3 : bond 0.00010 / 0.01 ( 1) link_ALPHA1-3 : angle 3.60759 / 1.89 ( 3) link_ALPHA1-6 : bond 0.00511 / 0.27 ( 1) link_ALPHA1-6 : angle 1.62143 / 0.92 ( 3) link_BETA1-4 : bond 0.00504 / 0.25 ( 3) link_BETA1-4 : angle 1.68223 / 0.94 ( 9) link_BETA1-6 : bond 0.00141 / 0.07 ( 1) link_BETA1-6 : angle 1.50402 / 0.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.272 Fit side-chains REVERT: B 12 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7864 (mmm-85) REVERT: B 52 LYS cc_start: 0.9409 (tttm) cc_final: 0.7325 (mptt) REVERT: B 150 GLU cc_start: 0.8643 (pm20) cc_final: 0.8290 (pm20) REVERT: C 79 GLN cc_start: 0.9153 (mm-40) cc_final: 0.8836 (mp10) REVERT: C 118 MET cc_start: 0.9357 (OUTLIER) cc_final: 0.9134 (ttp) REVERT: C 148 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (ppp) REVERT: A 41 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8906 (mt-10) REVERT: A 78 ASN cc_start: 0.7582 (p0) cc_final: 0.7210 (t0) REVERT: A 246 LYS cc_start: 0.9018 (mttp) cc_final: 0.8785 (mttm) REVERT: A 284 GLU cc_start: 0.8745 (tp30) cc_final: 0.8246 (tp30) outliers start: 10 outliers final: 7 residues processed: 112 average time/residue: 0.6061 time to fit residues: 71.1843 Evaluate side-chains 109 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain A residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [45, 41, 8, 78, 30, 13, 73, 21, 14, 76, 57] chunk 45 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3097 r_free = 0.3097 target = 0.093237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.077549 restraints weight = 10840.395| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.15 r_work: 0.2779 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6750 Z= 0.162 Angle : 0.561 14.110 9211 Z= 0.276 Chirality : 0.043 0.217 1066 Planarity : 0.004 0.057 1172 Dihedral : 6.016 54.758 1074 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.25 % Allowed : 18.52 % Favored : 80.22 % 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: -0.22 (0.28), residues: 816 helix: -1.86 (0.58), residues: 69 sheet: 0.65 (0.35), residues: 197 loop : -0.16 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 271 TYR 0.036 0.001 TYR B 31 PHE 0.011 0.001 PHE C 178 TRP 0.006 0.001 TRP A 248 HIS 0.002 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6743) covalent geometry : angle 0.55385 / 0.27 ( 9190) hydrogen bonds : bond 0.03174 / 2.08 ( 171) hydrogen bonds : angle 5.72358 / 3.93 ( 477) glycosidic custom : bond 0.00342 / 0.18 ( 1) glycosidic custom : angle 1.11533 / 0.60 ( 3) link_ALPHA1-3 : bond 0.00097 / 0.05 ( 1) link_ALPHA1-3 : angle 3.50900 / 1.84 ( 3) link_ALPHA1-6 : bond 0.00579 / 0.30 ( 1) link_ALPHA1-6 : angle 1.56076 / 0.88 ( 3) link_BETA1-4 : bond 0.00567 / 0.28 ( 3) link_BETA1-4 : angle 1.66438 / 0.94 ( 9) link_BETA1-6 : bond 0.00209 / 0.11 ( 1) link_BETA1-6 : angle 1.42485 / 0.74 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1632 Ramachandran restraints generated. 816 Oldfield, 0 Emsley, 816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.251 Fit side-chains REVERT: B 12 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7841 (mmm-85) REVERT: B 52 LYS cc_start: 0.9430 (tttm) cc_final: 0.7319 (mptt) REVERT: B 150 GLU cc_start: 0.8642 (pm20) cc_final: 0.8419 (pm20) REVERT: C 79 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8837 (mp10) REVERT: C 118 MET cc_start: 0.9353 (OUTLIER) cc_final: 0.9109 (ttp) REVERT: C 148 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8832 (ppp) REVERT: A 41 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8979 (mt-10) REVERT: A 78 ASN cc_start: 0.7552 (p0) cc_final: 0.7206 (t0) REVERT: A 246 LYS cc_start: 0.9003 (mttp) cc_final: 0.8768 (mttm) REVERT: A 284 GLU cc_start: 0.8749 (tp30) cc_final: 0.8255 (tp30) outliers start: 9 outliers final: 7 residues processed: 108 average time/residue: 0.5894 time to fit residues: 66.6563 Evaluate side-chains 111 residues out of total 718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 TYR Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain A residue 57 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [77, 62, 66, 30, 26, 68, 20, 31, 40, 73, 75] chunk 77 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 0.0040 chunk 73 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- 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 = 0.3085 r_free = 0.3085 target = 0.092464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.076801 restraints weight = 10867.154| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.13 r_work: 0.2777 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6750 Z= 0.212 Angle : 0.582 13.924 9211 Z= 0.287 Chirality : 0.044 0.225 1066 Planarity : 0.004 0.058 1172 Dihedral : 6.056 55.128 1074 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.39 % Allowed : 18.52 % Favored : 80.08 % 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: -0.22 (0.28), residues: 816 helix: -1.77 (0.58), residues: 69 sheet: 0.60 (0.35), residues: 198 loop : -0.16 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 271 TYR 0.013 0.001 TYR C 191 PHE 0.012 0.001 PHE C 178 TRP 0.006 0.001 TRP B 177 HIS 0.003 0.001 HIS B 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 ( 6743) covalent geometry : angle 0.57512 / 0.29 ( 9190) hydrogen bonds : bond 0.03357 / 2.21 ( 171) hydrogen bonds : angle 5.78546 / 3.97 ( 477) glycosidic custom : bond 0.00197 / 0.10 ( 1) glycosidic custom : angle 1.07298 / 0.58 ( 3) link_ALPHA1-3 : bond 0.00048 / 0.03 ( 1) link_ALPHA1-3 : angle 3.55238 / 1.86 ( 3) link_ALPHA1-6 : bond 0.00529 / 0.28 ( 1) link_ALPHA1-6 : angle 1.57761 / 0.89 ( 3) link_BETA1-4 : bond 0.00554 / 0.28 ( 3) link_BETA1-4 : angle 1.64413 / 0.92 ( 9) link_BETA1-6 : bond 0.00149 / 0.08 ( 1) link_BETA1-6 : angle 1.47911 / 0.77 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.35 seconds wall clock time: 45 minutes 24.36 seconds (2724.36 seconds total)