Starting phenix.real_space_refine on Thu Feb 13 14:50:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.map" model { file = "/net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e5g_27912/02_2025/8e5g_27912.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 20 7.16 5 S 55 5.16 5 C 5710 2.51 5 N 1510 2.21 5 O 1770 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9065 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1641 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 211} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, B, E, D Time building chain proxies: 4.48, per 1000 atoms: 0.49 Number of scatterers: 9065 At special positions: 0 Unit cell: (84.24, 71.28, 250.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 20 26.01 S 55 16.00 O 1770 8.00 N 1510 7.00 C 5710 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=71, symmetry=0 Number of additional bonds: simple=71, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.0 seconds 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 20.5% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.529A pdb=" N LYS A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS A 49 " --> pdb=" O CYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 49' Processing helix chain 'A' and resid 50 through 59 removed outlier: 3.795A pdb=" N ASN A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.524A pdb=" N ILE A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.998A pdb=" N CYS A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.529A pdb=" N LYS B 48 " --> pdb=" O PRO B 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS B 49 " --> pdb=" O CYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 50 through 59 removed outlier: 3.795A pdb=" N ASN B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 removed outlier: 3.524A pdb=" N ILE B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 181 through 186 removed outlier: 3.998A pdb=" N CYS B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.529A pdb=" N LYS C 48 " --> pdb=" O PRO C 45 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N CYS C 49 " --> pdb=" O CYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 45 through 49' Processing helix chain 'C' and resid 50 through 59 removed outlier: 3.796A pdb=" N ASN C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 86 removed outlier: 3.523A pdb=" N ILE C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 181 through 186 removed outlier: 3.998A pdb=" N CYS C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.529A pdb=" N LYS D 48 " --> pdb=" O PRO D 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS D 49 " --> pdb=" O CYS D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 50 through 59 removed outlier: 3.795A pdb=" N ASN D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.523A pdb=" N ILE D 77 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 181 through 186 removed outlier: 3.998A pdb=" N CYS D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.529A pdb=" N LYS E 48 " --> pdb=" O PRO E 45 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N CYS E 49 " --> pdb=" O CYS E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 49' Processing helix chain 'E' and resid 50 through 59 removed outlier: 3.795A pdb=" N ASN E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 86 removed outlier: 3.523A pdb=" N ILE E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'E' and resid 181 through 186 removed outlier: 3.998A pdb=" N CYS E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=2, first strand: chain 'A' and resid 194 through 210 removed outlier: 4.438A pdb=" N LYS A 195 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 238 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN A 197 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR A 236 " --> pdb=" O ASN A 197 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR A 199 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG A 234 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS A 201 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY A 232 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A 203 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 230 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU A 205 " --> pdb=" O TRP A 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP A 228 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 207 " --> pdb=" O THR A 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 226 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 247 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=4, first strand: chain 'B' and resid 194 through 210 removed outlier: 4.438A pdb=" N LYS B 195 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 238 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN B 197 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR B 236 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR B 199 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 234 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS B 201 " --> pdb=" O GLY B 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY B 232 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER B 203 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL B 230 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU B 205 " --> pdb=" O TRP B 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP B 228 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 207 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR B 226 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 247 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 95 through 96 Processing sheet with id=6, first strand: chain 'C' and resid 194 through 210 removed outlier: 4.438A pdb=" N LYS C 195 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 238 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN C 197 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR C 236 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR C 199 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG C 234 " --> pdb=" O THR C 199 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS C 201 " --> pdb=" O GLY C 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY C 232 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 203 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL C 230 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU C 205 " --> pdb=" O TRP C 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP C 228 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 207 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 226 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 247 " --> pdb=" O PHE C 239 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 95 through 96 Processing sheet with id=8, first strand: chain 'D' and resid 194 through 210 removed outlier: 4.438A pdb=" N LYS D 195 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 238 " --> pdb=" O LYS D 195 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN D 197 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR D 236 " --> pdb=" O ASN D 197 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N THR D 199 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG D 234 " --> pdb=" O THR D 199 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LYS D 201 " --> pdb=" O GLY D 232 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N GLY D 232 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER D 203 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL D 230 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU D 205 " --> pdb=" O TRP D 228 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TRP D 228 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 207 " --> pdb=" O THR D 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 226 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER D 247 " --> pdb=" O PHE D 239 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 95 through 96 Processing sheet with id=10, first strand: chain 'E' and resid 194 through 210 removed outlier: 4.437A pdb=" N LYS E 195 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL E 238 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN E 197 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N THR E 236 " --> pdb=" O ASN E 197 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N THR E 199 " --> pdb=" O ARG E 234 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG E 234 " --> pdb=" O THR E 199 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS E 201 " --> pdb=" O GLY E 232 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N GLY E 232 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER E 203 " --> pdb=" O VAL E 230 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL E 230 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N GLU E 205 " --> pdb=" O TRP E 228 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TRP E 228 " --> pdb=" O GLU E 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 207 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 226 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER E 247 " --> pdb=" O PHE E 239 " (cutoff:3.500A) 130 hydrogen bonds defined for protein. 375 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 3964 1.38 - 1.56: 5296 1.56 - 1.74: 10 1.74 - 1.91: 65 1.91 - 2.09: 80 Bond restraints: 9415 Sorted by residual: bond pdb=" N GLU B 205 " pdb=" CA GLU B 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.93e+01 bond pdb=" N GLU E 205 " pdb=" CA GLU E 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.92e+01 bond pdb=" N GLU D 205 " pdb=" CA GLU D 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.92e+01 bond pdb=" N GLU A 205 " pdb=" CA GLU A 205 " ideal model delta sigma weight residual 1.457 1.557 -0.099 1.29e-02 6.01e+03 5.91e+01 bond pdb=" N GLU C 205 " pdb=" CA GLU C 205 " ideal model delta sigma weight residual 1.457 1.556 -0.099 1.29e-02 6.01e+03 5.90e+01 ... (remaining 9410 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12756 2.68 - 5.35: 304 5.35 - 8.03: 55 8.03 - 10.71: 25 10.71 - 13.38: 5 Bond angle restraints: 13145 Sorted by residual: angle pdb=" N ASN E 207 " pdb=" CA ASN E 207 " pdb=" C ASN E 207 " ideal model delta sigma weight residual 109.29 122.67 -13.38 1.41e+00 5.03e-01 9.01e+01 angle pdb=" N ASN D 207 " pdb=" CA ASN D 207 " pdb=" C ASN D 207 " ideal model delta sigma weight residual 109.29 122.67 -13.38 1.41e+00 5.03e-01 9.00e+01 angle pdb=" N ASN A 207 " pdb=" CA ASN A 207 " pdb=" C ASN A 207 " ideal model delta sigma weight residual 109.29 122.64 -13.35 1.41e+00 5.03e-01 8.97e+01 angle pdb=" N ASN B 207 " pdb=" CA ASN B 207 " pdb=" C ASN B 207 " ideal model delta sigma weight residual 109.29 122.63 -13.34 1.41e+00 5.03e-01 8.95e+01 angle pdb=" N ASN C 207 " pdb=" CA ASN C 207 " pdb=" C ASN C 207 " ideal model delta sigma weight residual 109.29 122.62 -13.33 1.41e+00 5.03e-01 8.94e+01 ... (remaining 13140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 4280 16.78 - 33.56: 475 33.56 - 50.33: 85 50.33 - 67.11: 45 67.11 - 83.89: 40 Dihedral angle restraints: 4925 sinusoidal: 1820 harmonic: 3105 Sorted by residual: dihedral pdb=" N ASN D 207 " pdb=" C ASN D 207 " pdb=" CA ASN D 207 " pdb=" CB ASN D 207 " ideal model delta harmonic sigma weight residual 122.80 151.68 -28.88 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N ASN E 207 " pdb=" C ASN E 207 " pdb=" CA ASN E 207 " pdb=" CB ASN E 207 " ideal model delta harmonic sigma weight residual 122.80 151.65 -28.85 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N ASN A 207 " pdb=" C ASN A 207 " pdb=" CA ASN A 207 " pdb=" CB ASN A 207 " ideal model delta harmonic sigma weight residual 122.80 151.62 -28.82 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 4922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.242: 1255 0.242 - 0.484: 0 0.484 - 0.726: 5 0.726 - 0.968: 0 0.968 - 1.210: 5 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ASN D 207 " pdb=" N ASN D 207 " pdb=" C ASN D 207 " pdb=" CB ASN D 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.66e+01 chirality pdb=" CA ASN E 207 " pdb=" N ASN E 207 " pdb=" C ASN E 207 " pdb=" CB ASN E 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.65e+01 chirality pdb=" CA ASN A 207 " pdb=" N ASN A 207 " pdb=" C ASN A 207 " pdb=" CB ASN A 207 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.64e+01 ... (remaining 1262 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC D 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC D 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC D 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC D 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC D 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC D 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC D 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC D 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC D 301 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC C 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC C 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC C 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC C 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC C 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC C 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC C 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC C 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC C 301 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC E 301 " -0.011 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC E 301 " 0.084 2.00e-02 2.50e+03 pdb=" C3C HEC E 301 " -0.001 2.00e-02 2.50e+03 pdb=" C4C HEC E 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC E 301 " -0.019 2.00e-02 2.50e+03 pdb=" CHC HEC E 301 " -0.014 2.00e-02 2.50e+03 pdb=" CHD HEC E 301 " -0.001 2.00e-02 2.50e+03 pdb=" CMC HEC E 301 " -0.029 2.00e-02 2.50e+03 pdb=" NC HEC E 301 " -0.005 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 161 2.51 - 3.11: 7232 3.11 - 3.71: 14229 3.71 - 4.30: 19688 4.30 - 4.90: 30611 Nonbonded interactions: 71921 Sorted by model distance: nonbonded pdb=" ND2 ASN A 197 " pdb=" ND2 ASN D 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN B 197 " pdb=" ND2 ASN C 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN D 197 " pdb=" ND2 ASN E 207 " model vdw 1.918 3.200 nonbonded pdb=" ND2 ASN A 207 " pdb=" ND2 ASN C 197 " model vdw 1.918 3.200 nonbonded pdb=" CD1 ILE D 37 " pdb=" O1A HEC E 303 " model vdw 2.016 3.460 ... (remaining 71916 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.700 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.006 0.099 9415 Z= 0.413 Angle : 1.052 13.382 13145 Z= 0.580 Chirality : 0.097 1.210 1265 Planarity : 0.005 0.035 1655 Dihedral : 17.243 83.885 2965 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 47.42 Ramachandran Plot: Outliers : 0.46 % Allowed : 9.63 % Favored : 89.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 1.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.25), residues: 1090 helix: 1.43 (0.42), residues: 145 sheet: -0.68 (0.50), residues: 100 loop : -2.43 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 34 HIS 0.006 0.001 HIS E 189 PHE 0.006 0.002 PHE D 239 TYR 0.015 0.002 TYR B 223 ARG 0.001 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7276 (tp30) cc_final: 0.6110 (mm-30) REVERT: C 59 ASN cc_start: 0.8837 (t0) cc_final: 0.8261 (t0) REVERT: C 65 LYS cc_start: 0.8241 (ptpt) cc_final: 0.7998 (ptpt) REVERT: D 65 LYS cc_start: 0.8297 (ptpt) cc_final: 0.8025 (ptpt) REVERT: E 65 LYS cc_start: 0.8267 (ptpt) cc_final: 0.8059 (ptpt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2377 time to fit residues: 46.6057 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 43 ASN B 60 ASN C 64 HIS D 64 HIS E 64 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.096547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.077097 restraints weight = 28932.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.079868 restraints weight = 16634.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.081719 restraints weight = 11826.053| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9415 Z= 0.377 Angle : 0.953 14.756 13145 Z= 0.376 Chirality : 0.043 0.142 1265 Planarity : 0.003 0.026 1655 Dihedral : 15.532 89.986 1325 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.53 % Favored : 91.01 % Rotamer: Outliers : 1.84 % Allowed : 10.34 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.26), residues: 1090 helix: 0.44 (0.38), residues: 160 sheet: -2.10 (0.38), residues: 145 loop : -2.16 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 34 HIS 0.008 0.001 HIS A 64 PHE 0.014 0.002 PHE D 138 TYR 0.019 0.002 TYR A 223 ARG 0.003 0.001 ARG A 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 33 MET cc_start: 0.6625 (mpp) cc_final: 0.6280 (mpp) REVERT: C 59 ASN cc_start: 0.8912 (t0) cc_final: 0.7971 (t0) REVERT: C 60 ASN cc_start: 0.8798 (t0) cc_final: 0.8542 (t0) REVERT: C 65 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7814 (ptpt) outliers start: 16 outliers final: 13 residues processed: 131 average time/residue: 0.2094 time to fit residues: 38.3937 Evaluate side-chains 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.0470 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN C 43 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.096995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077605 restraints weight = 29152.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080405 restraints weight = 16597.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.082297 restraints weight = 11782.951| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9415 Z= 0.260 Angle : 0.851 14.671 13145 Z= 0.324 Chirality : 0.041 0.120 1265 Planarity : 0.003 0.026 1655 Dihedral : 15.348 89.636 1325 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.25 % Favored : 92.29 % Rotamer: Outliers : 2.18 % Allowed : 13.10 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 1090 helix: 0.28 (0.39), residues: 160 sheet: -2.24 (0.37), residues: 145 loop : -2.10 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 228 HIS 0.003 0.001 HIS B 108 PHE 0.013 0.002 PHE D 138 TYR 0.013 0.001 TYR A 223 ARG 0.001 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7864 (ptpt) REVERT: D 65 LYS cc_start: 0.8301 (ptpt) cc_final: 0.8017 (mttt) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.2025 time to fit residues: 36.0503 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 179 ILE Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 45 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.096849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.077410 restraints weight = 28908.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080181 restraints weight = 16686.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.082042 restraints weight = 11894.330| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9415 Z= 0.264 Angle : 0.853 14.526 13145 Z= 0.321 Chirality : 0.041 0.125 1265 Planarity : 0.003 0.026 1655 Dihedral : 15.360 89.845 1325 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.16 % Favored : 92.39 % Rotamer: Outliers : 3.33 % Allowed : 16.21 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.26), residues: 1090 helix: 0.38 (0.40), residues: 160 sheet: -2.28 (0.36), residues: 145 loop : -2.12 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 228 HIS 0.003 0.001 HIS B 108 PHE 0.016 0.002 PHE E 54 TYR 0.013 0.001 TYR E 152 ARG 0.002 0.000 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.9163 (p0) cc_final: 0.8784 (p0) REVERT: C 196 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9178 (pt) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.2036 time to fit residues: 37.0619 Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077490 restraints weight = 29154.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080234 restraints weight = 16770.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082087 restraints weight = 12004.893| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9415 Z= 0.264 Angle : 0.851 14.079 13145 Z= 0.319 Chirality : 0.041 0.133 1265 Planarity : 0.003 0.027 1655 Dihedral : 15.373 89.228 1325 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.34 % Favored : 92.20 % Rotamer: Outliers : 3.68 % Allowed : 17.47 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.26), residues: 1090 helix: 0.66 (0.41), residues: 160 sheet: -2.42 (0.36), residues: 145 loop : -2.14 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 228 HIS 0.003 0.001 HIS B 108 PHE 0.018 0.002 PHE E 54 TYR 0.012 0.001 TYR B 152 ARG 0.001 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8537 (ptpt) REVERT: D 221 THR cc_start: 0.8418 (p) cc_final: 0.8191 (t) REVERT: E 48 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8275 (ttpt) outliers start: 32 outliers final: 24 residues processed: 131 average time/residue: 0.1919 time to fit residues: 35.9056 Evaluate side-chains 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.096133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076791 restraints weight = 29077.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.079536 restraints weight = 16864.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081369 restraints weight = 12076.353| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9415 Z= 0.299 Angle : 0.876 14.922 13145 Z= 0.328 Chirality : 0.041 0.183 1265 Planarity : 0.003 0.029 1655 Dihedral : 15.328 89.594 1325 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.26 % Favored : 91.38 % Rotamer: Outliers : 4.71 % Allowed : 17.93 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.26), residues: 1090 helix: 0.63 (0.40), residues: 160 sheet: -2.47 (0.36), residues: 145 loop : -2.20 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 34 HIS 0.003 0.001 HIS E 32 PHE 0.021 0.002 PHE E 54 TYR 0.015 0.001 TYR B 152 ARG 0.002 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8280 (ptpt) REVERT: D 221 THR cc_start: 0.8436 (p) cc_final: 0.8234 (t) REVERT: E 48 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7921 (ttmm) REVERT: E 65 LYS cc_start: 0.7725 (mttt) cc_final: 0.7467 (mttt) REVERT: E 76 HIS cc_start: 0.8410 (m170) cc_final: 0.7847 (m-70) outliers start: 41 outliers final: 23 residues processed: 135 average time/residue: 0.1956 time to fit residues: 37.6608 Evaluate side-chains 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 97 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076694 restraints weight = 29624.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.079424 restraints weight = 16979.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.081291 restraints weight = 12124.821| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9415 Z= 0.315 Angle : 0.895 15.500 13145 Z= 0.341 Chirality : 0.042 0.154 1265 Planarity : 0.003 0.031 1655 Dihedral : 15.352 89.541 1325 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.07 % Favored : 91.56 % Rotamer: Outliers : 4.14 % Allowed : 19.54 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.25), residues: 1090 helix: 0.54 (0.40), residues: 160 sheet: -2.57 (0.35), residues: 145 loop : -2.27 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 34 HIS 0.003 0.001 HIS E 32 PHE 0.028 0.002 PHE E 54 TYR 0.015 0.001 TYR D 152 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 47 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8155 (mp0) REVERT: E 48 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7829 (ttmm) REVERT: E 65 LYS cc_start: 0.7728 (mttt) cc_final: 0.7494 (mttt) REVERT: E 76 HIS cc_start: 0.8388 (m170) cc_final: 0.7774 (m170) outliers start: 36 outliers final: 24 residues processed: 136 average time/residue: 0.2030 time to fit residues: 39.2647 Evaluate side-chains 122 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 121 PHE Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.095646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.076218 restraints weight = 30165.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078969 restraints weight = 17321.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.080821 restraints weight = 12361.694| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9415 Z= 0.331 Angle : 0.939 20.165 13145 Z= 0.352 Chirality : 0.042 0.147 1265 Planarity : 0.003 0.031 1655 Dihedral : 15.420 89.476 1325 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.62 % Favored : 90.46 % Rotamer: Outliers : 4.48 % Allowed : 20.23 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.25), residues: 1090 helix: 0.11 (0.38), residues: 165 sheet: -2.18 (0.37), residues: 130 loop : -2.38 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 34 HIS 0.004 0.001 HIS D 189 PHE 0.054 0.003 PHE E 54 TYR 0.015 0.002 TYR A 152 ARG 0.003 0.000 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.6898 (tptp) cc_final: 0.6624 (tptp) REVERT: B 65 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8541 (ptpt) REVERT: B 72 ASP cc_start: 0.9186 (p0) cc_final: 0.8930 (p0) REVERT: B 76 HIS cc_start: 0.8294 (m170) cc_final: 0.7816 (m-70) REVERT: E 48 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (ttmm) REVERT: E 65 LYS cc_start: 0.7762 (mttt) cc_final: 0.7545 (mttt) REVERT: E 76 HIS cc_start: 0.8483 (m170) cc_final: 0.7805 (m170) REVERT: E 221 THR cc_start: 0.8258 (p) cc_final: 0.8020 (t) outliers start: 39 outliers final: 24 residues processed: 132 average time/residue: 0.2016 time to fit residues: 38.0984 Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 5 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.093859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074990 restraints weight = 29916.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.077712 restraints weight = 17210.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079443 restraints weight = 12329.114| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 9415 Z= 0.424 Angle : 1.039 23.668 13145 Z= 0.386 Chirality : 0.044 0.193 1265 Planarity : 0.003 0.032 1655 Dihedral : 15.504 88.997 1325 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.00 % Favored : 89.08 % Rotamer: Outliers : 3.91 % Allowed : 21.03 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.25), residues: 1090 helix: -0.09 (0.38), residues: 165 sheet: -2.36 (0.36), residues: 130 loop : -2.45 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.006 0.001 HIS D 189 PHE 0.063 0.003 PHE E 54 TYR 0.022 0.002 TYR A 152 ARG 0.006 0.001 ARG D 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 90 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LYS cc_start: 0.7126 (tptp) cc_final: 0.6848 (tptp) REVERT: A 202 VAL cc_start: 0.6292 (t) cc_final: 0.6058 (t) REVERT: B 65 LYS cc_start: 0.8858 (ptpt) cc_final: 0.8402 (ptpt) REVERT: B 72 ASP cc_start: 0.9184 (p0) cc_final: 0.8875 (p0) REVERT: B 76 HIS cc_start: 0.8568 (m170) cc_final: 0.8087 (m-70) REVERT: D 60 ASN cc_start: 0.8440 (t0) cc_final: 0.7890 (t0) REVERT: D 138 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: E 48 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7979 (ttmm) REVERT: E 65 LYS cc_start: 0.7747 (mttt) cc_final: 0.7525 (mttt) REVERT: E 76 HIS cc_start: 0.8520 (m170) cc_final: 0.7851 (m170) REVERT: E 221 THR cc_start: 0.8152 (p) cc_final: 0.7932 (t) outliers start: 34 outliers final: 25 residues processed: 118 average time/residue: 0.1907 time to fit residues: 32.7000 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 9.9990 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 54 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.097091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077823 restraints weight = 29567.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080560 restraints weight = 17187.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.082403 restraints weight = 12330.790| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9415 Z= 0.267 Angle : 0.940 20.122 13145 Z= 0.348 Chirality : 0.042 0.241 1265 Planarity : 0.003 0.032 1655 Dihedral : 15.251 88.185 1325 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.17 % Favored : 90.92 % Rotamer: Outliers : 3.10 % Allowed : 21.49 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.25), residues: 1090 helix: 0.12 (0.40), residues: 165 sheet: -2.38 (0.36), residues: 130 loop : -2.40 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 228 HIS 0.006 0.001 HIS A 189 PHE 0.048 0.002 PHE E 54 TYR 0.014 0.001 TYR C 152 ARG 0.002 0.000 ARG D 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2180 Ramachandran restraints generated. 1090 Oldfield, 0 Emsley, 1090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8807 (ptpt) cc_final: 0.8332 (ptpt) REVERT: B 72 ASP cc_start: 0.9200 (p0) cc_final: 0.8964 (p0) REVERT: D 60 ASN cc_start: 0.8410 (t0) cc_final: 0.7604 (t0) REVERT: D 138 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6639 (m-80) REVERT: E 48 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: E 65 LYS cc_start: 0.7727 (mttt) cc_final: 0.7489 (mttt) REVERT: E 76 HIS cc_start: 0.8473 (m170) cc_final: 0.7820 (m170) outliers start: 27 outliers final: 24 residues processed: 118 average time/residue: 0.1929 time to fit residues: 33.0959 Evaluate side-chains 115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 200 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 64 HIS Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 84 CYS Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain C residue 200 HIS Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 84 CYS Chi-restraints excluded: chain D residue 138 PHE Chi-restraints excluded: chain D residue 200 HIS Chi-restraints excluded: chain D residue 221 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 84 CYS Chi-restraints excluded: chain E residue 121 PHE Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain E residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.094968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076389 restraints weight = 28826.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.079193 restraints weight = 15726.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.081070 restraints weight = 10936.226| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 9415 Z= 0.325 Angle : 0.999 23.668 13145 Z= 0.358 Chirality : 0.043 0.269 1265 Planarity : 0.003 0.033 1655 Dihedral : 15.321 89.021 1325 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.00 % Favored : 89.17 % Rotamer: Outliers : 3.10 % Allowed : 22.07 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.25), residues: 1090 helix: 0.06 (0.39), residues: 165 sheet: -2.55 (0.35), residues: 130 loop : -2.46 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 198 HIS 0.011 0.001 HIS A 189 PHE 0.052 0.003 PHE E 54 TYR 0.016 0.002 TYR A 152 ARG 0.002 0.000 ARG D 78 =============================================================================== Job complete usr+sys time: 2634.55 seconds wall clock time: 48 minutes 23.76 seconds (2903.76 seconds total)