Starting phenix.real_space_refine on Thu Jul 2 22:38:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2026/7rpw_24624.cif" } resolution = 4.38 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= 0.001 sd= 0.101 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 S 25 5.16 5 C 6567 2.51 5 N 1750 2.21 5 O 2185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10594 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1941 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "X" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 409 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "Z" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 3480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3480 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 425} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.36, per 1000 atoms: 0.22 Number of scatterers: 10594 At special positions: 0 Unit cell: (117, 106.5, 123, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 25 16.00 P 63 15.00 O 2185 8.00 N 1750 7.00 C 6567 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 302.9 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 15 sheets defined 28.1% alpha, 16.5% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.712A pdb=" N ILE A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.864A pdb=" N ASN A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.501A pdb=" N VAL B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 removed outlier: 4.131A pdb=" N LEU B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.584A pdb=" N VAL B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.705A pdb=" N ASP C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU C 18 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 79 removed outlier: 3.662A pdb=" N ILE C 77 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS C 79 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 4.070A pdb=" N LYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 removed outlier: 4.706A pdb=" N ILE E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 removed outlier: 3.804A pdb=" N THR E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 47 Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.522A pdb=" N LEU E 54 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 90 through 97 removed outlier: 3.840A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 133 removed outlier: 4.304A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 removed outlier: 4.557A pdb=" N LEU E 142 " --> pdb=" O GLY E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 4.067A pdb=" N ARG E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 189 removed outlier: 3.514A pdb=" N VAL E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 204 removed outlier: 4.544A pdb=" N ILE E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 217 Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 291 through 300 removed outlier: 4.118A pdb=" N TYR E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 331 removed outlier: 4.102A pdb=" N HIS E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG E 330 " --> pdb=" O GLU E 326 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 375 removed outlier: 3.636A pdb=" N GLU E 373 " --> pdb=" O ARG E 369 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.646A pdb=" N ILE A 89 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A 92 " --> pdb=" O LYS A 99 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS A 99 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU C 175 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 112 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C 173 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52 removed outlier: 4.116A pdb=" N ILE A 35 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 27 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N LEU A 40 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N SER A 25 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 70 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 28 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138 removed outlier: 3.622A pdb=" N VAL A 134 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.603A pdb=" N ALA A 179 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.670A pdb=" N THR B 99 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.630A pdb=" N ASP B 49 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE B 51 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N TYR B 236 " --> pdb=" O PHE B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 190 removed outlier: 3.694A pdb=" N SER B 189 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS B 132 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AB1, first strand: chain 'B' and resid 165 through 168 removed outlier: 3.620A pdb=" N PHE B 165 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 97 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 87 " --> pdb=" O TYR C 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 5 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29 removed outlier: 4.749A pdb=" N VAL C 26 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL C 37 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 51 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU C 46 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.516A pdb=" N PHE C 218 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.890A pdb=" N SER C 192 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 241 removed outlier: 6.364A pdb=" N GLU E 239 " --> pdb=" O LYS E 433 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 278 removed outlier: 4.203A pdb=" N ILE E 307 " --> pdb=" O ILE E 268 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE E 306 " --> pdb=" O MET E 353 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.43 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2810 1.33 - 1.45: 1960 1.45 - 1.57: 5949 1.57 - 1.69: 122 1.69 - 1.81: 50 Bond restraints: 10891 Sorted by residual: bond pdb=" C3' DC Z 26 " pdb=" C2' DC Z 26 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 9.06e+00 bond pdb=" C3' DT Z 30 " pdb=" C2' DT Z 30 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 bond pdb=" C4' DG Y 4 " pdb=" C3' DG Y 4 " ideal model delta sigma weight residual 1.529 1.502 0.027 1.00e-02 1.00e+04 7.13e+00 bond pdb=" C3' DA X 16 " pdb=" C2' DA X 16 " ideal model delta sigma weight residual 1.516 1.536 -0.020 8.00e-03 1.56e+04 6.39e+00 ... (remaining 10886 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 14182 1.25 - 2.50: 631 2.50 - 3.75: 111 3.75 - 5.00: 24 5.00 - 6.25: 6 Bond angle restraints: 14954 Sorted by residual: angle pdb=" O4' DG Y 5 " pdb=" C1' DG Y 5 " pdb=" N9 DG Y 5 " ideal model delta sigma weight residual 108.00 111.25 -3.25 7.00e-01 2.04e+00 2.16e+01 angle pdb=" N3 DT Z 32 " pdb=" C4 DT Z 32 " pdb=" O4 DT Z 32 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" O4' DG Y 4 " pdb=" C4' DG Y 4 " pdb=" C3' DG Y 4 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT Z 37 " pdb=" C4 DT Z 37 " pdb=" O4 DT Z 37 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 ... (remaining 14949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.68: 6066 34.68 - 69.36: 385 69.36 - 104.04: 5 104.04 - 138.72: 0 138.72 - 173.39: 5 Dihedral angle restraints: 6461 sinusoidal: 3029 harmonic: 3432 Sorted by residual: dihedral pdb=" CA SER E 139 " pdb=" C SER E 139 " pdb=" N ARG E 140 " pdb=" CA ARG E 140 " ideal model delta harmonic sigma weight residual 180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LEU C 205 " pdb=" C LEU C 205 " pdb=" N SER C 206 " pdb=" CA SER C 206 " ideal model delta harmonic sigma weight residual 180.00 157.66 22.34 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU C 11 " pdb=" C LEU C 11 " pdb=" N LYS C 12 " pdb=" CA LYS C 12 " ideal model delta harmonic sigma weight residual 180.00 159.44 20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 6458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1122 0.035 - 0.069: 402 0.069 - 0.104: 130 0.104 - 0.139: 66 0.139 - 0.173: 4 Chirality restraints: 1724 Sorted by residual: chirality pdb=" CB VAL C 244 " pdb=" CA VAL C 244 " pdb=" CG1 VAL C 244 " pdb=" CG2 VAL C 244 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" C3' DA Z 22 " pdb=" C4' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" C2' DA Z 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" P DG Z 27 " pdb=" OP1 DG Z 27 " pdb=" OP2 DG Z 27 " pdb=" O5' DG Z 27 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1721 not shown) Planarity restraints: 1681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 93 " 0.019 5.00e-02 4.00e+02 2.94e-02 1.39e+00 pdb=" N PRO C 94 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 226 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO E 227 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 121 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO B 122 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.016 5.00e-02 4.00e+02 ... (remaining 1678 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.38: 62 2.38 - 3.01: 6110 3.01 - 3.64: 17020 3.64 - 4.27: 23587 4.27 - 4.90: 36833 Nonbonded interactions: 83612 Sorted by model distance: nonbonded pdb=" O GLY E 60 " pdb="MN MN X 101 " model vdw 1.756 2.320 nonbonded pdb=" OP1 DG X 22 " pdb="MN MN E 701 " model vdw 1.835 2.320 nonbonded pdb=" O3' DG X 20 " pdb="MN MN X 101 " model vdw 1.913 2.320 nonbonded pdb=" O LYS E 130 " pdb=" OG1 THR E 134 " model vdw 2.077 3.040 nonbonded pdb=" OP1 DC X 21 " pdb="MN MN X 102 " model vdw 2.146 2.320 ... (remaining 83607 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=0.50 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: 0.550 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.030 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 0.052 10892 Z= 0.285 Angle : 0.621 6.255 14954 Z= 0.436 Chirality : 0.044 0.173 1724 Planarity : 0.003 0.029 1681 Dihedral : 19.295 173.395 4243 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.27 % Favored : 88.64 % Rotamer: Outliers : 9.97 % Allowed : 13.46 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.24), residues: 1171 helix: -0.42 (0.30), residues: 300 sheet: -1.68 (0.31), residues: 304 loop : -2.82 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 265 TYR 0.010 0.001 TYR C 196 PHE 0.018 0.001 PHE E 53 TRP 0.003 0.001 TRP E 50 HIS 0.005 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.28 (10891) covalent geometry : angle 0.62131 / 0.44 (14954) hydrogen bonds : bond 0.21083 / 14.20 ( 388) hydrogen bonds : angle 9.19799 / 6.35 ( 1006) Misc. bond : bond 0.05188 / 2.73 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 153 time to evaluate : 0.259 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: A 37 SER cc_start: 0.8093 (t) cc_final: 0.7566 (m) REVERT: A 80 SER cc_start: 0.9022 (t) cc_final: 0.8779 (p) REVERT: A 137 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8102 (t) REVERT: B 21 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7684 (t0) REVERT: B 89 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4884 (tp) REVERT: C 44 ILE cc_start: 0.9077 (mt) cc_final: 0.8816 (mm) REVERT: C 75 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7341 (tpp) REVERT: C 146 VAL cc_start: 0.7875 (t) cc_final: 0.6797 (t) REVERT: E 123 GLU cc_start: 0.7720 (pp20) cc_final: 0.7429 (mp0) REVERT: E 142 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (mp) REVERT: E 164 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7697 (tpt170) REVERT: E 328 MET cc_start: 0.8600 (mtm) cc_final: 0.7994 (tmm) REVERT: E 360 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4463 (t80) REVERT: E 372 LEU cc_start: 0.6464 (tp) cc_final: 0.6179 (tp) outliers start: 103 outliers final: 40 residues processed: 239 average time/residue: 0.0799 time to fit residues: 27.3904 Evaluate side-chains 149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.2980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 ASN E 391 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.113562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.095488 restraints weight = 46762.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096226 restraints weight = 36427.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.096661 restraints weight = 34844.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.096979 restraints weight = 26315.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.097651 restraints weight = 24204.029| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3946 r_free = 0.3946 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10892 Z= 0.194 Angle : 0.724 7.876 14954 Z= 0.397 Chirality : 0.050 0.311 1724 Planarity : 0.005 0.056 1681 Dihedral : 22.219 172.644 1931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.36 % Favored : 88.56 % Rotamer: Outliers : 0.39 % Allowed : 3.78 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.23), residues: 1171 helix: -0.71 (0.28), residues: 307 sheet: -1.64 (0.30), residues: 316 loop : -2.93 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 107 TYR 0.020 0.002 TYR E 360 PHE 0.030 0.002 PHE B 60 TRP 0.017 0.003 TRP E 50 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (10891) covalent geometry : angle 0.72388 / 0.40 (14954) hydrogen bonds : bond 0.06158 / 4.16 ( 388) hydrogen bonds : angle 7.57436 / 5.24 ( 1006) Misc. bond : bond 0.00304 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 SER cc_start: 0.9041 (t) cc_final: 0.8807 (p) REVERT: B 146 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6575 (mt-10) REVERT: B 216 GLU cc_start: 0.4298 (mm-30) cc_final: 0.3990 (mm-30) REVERT: C 1 MET cc_start: 0.7566 (tpt) cc_final: 0.7210 (tpp) REVERT: C 44 ILE cc_start: 0.8825 (mt) cc_final: 0.8623 (mm) REVERT: C 146 VAL cc_start: 0.6962 (t) cc_final: 0.6528 (t) REVERT: C 220 ASN cc_start: 0.7701 (m-40) cc_final: 0.7189 (m-40) REVERT: E 8 GLU cc_start: 0.7784 (tm-30) cc_final: 0.6846 (pt0) REVERT: E 63 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7435 (mt-10) REVERT: E 133 LEU cc_start: 0.7632 (mp) cc_final: 0.7218 (mt) REVERT: E 164 ARG cc_start: 0.7842 (mtt180) cc_final: 0.7590 (tpt170) REVERT: E 280 ARG cc_start: 0.6538 (tmt170) cc_final: 0.5880 (tpt90) REVERT: E 328 MET cc_start: 0.8402 (mtm) cc_final: 0.8053 (tmm) REVERT: E 372 LEU cc_start: 0.6332 (tp) cc_final: 0.6052 (tp) outliers start: 4 outliers final: 1 residues processed: 159 average time/residue: 0.0895 time to fit residues: 20.1163 Evaluate side-chains 97 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 116 optimal weight: 7.9990 chunk 115 optimal weight: 30.0000 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.0770 chunk 73 optimal weight: 30.0000 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 0.0050 chunk 35 optimal weight: 0.0870 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.117964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.099775 restraints weight = 46280.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.101165 restraints weight = 34393.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.101646 restraints weight = 28467.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.101853 restraints weight = 22690.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.102056 restraints weight = 21870.811| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10892 Z= 0.146 Angle : 0.662 7.786 14954 Z= 0.360 Chirality : 0.049 0.334 1724 Planarity : 0.004 0.037 1681 Dihedral : 22.224 174.239 1931 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.31 % Favored : 90.61 % Rotamer: Outliers : 0.19 % Allowed : 3.48 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.97 (0.23), residues: 1171 helix: -0.76 (0.28), residues: 309 sheet: -1.60 (0.30), residues: 313 loop : -2.94 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 36 TYR 0.037 0.002 TYR C 59 PHE 0.021 0.002 PHE C 176 TRP 0.014 0.002 TRP E 50 HIS 0.003 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (10891) covalent geometry : angle 0.66165 / 0.36 (14954) hydrogen bonds : bond 0.04680 / 3.12 ( 388) hydrogen bonds : angle 6.89857 / 4.74 ( 1006) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.7536 (mp) cc_final: 0.6949 (mp) REVERT: A 80 SER cc_start: 0.8996 (t) cc_final: 0.8787 (p) REVERT: A 163 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8430 (mp0) REVERT: B 126 ASN cc_start: 0.7149 (t0) cc_final: 0.6928 (t0) REVERT: B 136 LEU cc_start: 0.6746 (tp) cc_final: 0.6391 (tp) REVERT: B 146 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5723 (tt0) REVERT: C 1 MET cc_start: 0.7510 (tpt) cc_final: 0.7118 (tpp) REVERT: C 44 ILE cc_start: 0.8844 (mt) cc_final: 0.8559 (mm) REVERT: C 75 MET cc_start: 0.7716 (mtt) cc_final: 0.7374 (tpp) REVERT: C 146 VAL cc_start: 0.7074 (t) cc_final: 0.6825 (t) REVERT: C 220 ASN cc_start: 0.8148 (m-40) cc_final: 0.7676 (m-40) REVERT: E 8 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6729 (pt0) REVERT: E 63 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7391 (mt-10) REVERT: E 123 GLU cc_start: 0.7564 (mm-30) cc_final: 0.7360 (mm-30) REVERT: E 142 LEU cc_start: 0.7610 (mp) cc_final: 0.7410 (tt) REVERT: E 164 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7314 (tpt170) REVERT: E 259 TYR cc_start: 0.8399 (t80) cc_final: 0.7917 (t80) REVERT: E 328 MET cc_start: 0.8521 (mtm) cc_final: 0.8146 (tmm) REVERT: E 340 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5548 (mt) REVERT: E 372 LEU cc_start: 0.6267 (tp) cc_final: 0.6001 (tp) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.0914 time to fit residues: 17.7423 Evaluate side-chains 99 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 30.0000 chunk 39 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.117842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.099589 restraints weight = 46522.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.100509 restraints weight = 40689.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.101120 restraints weight = 35551.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.101640 restraints weight = 26048.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.102132 restraints weight = 23706.248| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10892 Z= 0.133 Angle : 0.646 11.171 14954 Z= 0.348 Chirality : 0.048 0.329 1724 Planarity : 0.004 0.067 1681 Dihedral : 22.237 174.700 1931 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.56 % Favored : 90.35 % Rotamer: Outliers : 0.19 % Allowed : 4.16 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.23), residues: 1171 helix: -0.51 (0.29), residues: 299 sheet: -1.68 (0.30), residues: 309 loop : -2.89 (0.23), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 44 TYR 0.026 0.002 TYR C 59 PHE 0.020 0.001 PHE C 228 TRP 0.014 0.002 TRP E 50 HIS 0.004 0.001 HIS E 386 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10891) covalent geometry : angle 0.64643 / 0.35 (14954) hydrogen bonds : bond 0.04252 / 2.85 ( 388) hydrogen bonds : angle 6.57836 / 4.53 ( 1006) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 126 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.7453 (t80) cc_final: 0.7223 (t80) REVERT: A 163 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8447 (mp0) REVERT: B 146 GLU cc_start: 0.6222 (mt-10) cc_final: 0.5565 (tt0) REVERT: C 44 ILE cc_start: 0.8880 (mt) cc_final: 0.8638 (mm) REVERT: C 65 PHE cc_start: 0.8437 (t80) cc_final: 0.8129 (t80) REVERT: C 75 MET cc_start: 0.7613 (mtt) cc_final: 0.7372 (tpp) REVERT: C 146 VAL cc_start: 0.7463 (t) cc_final: 0.7200 (t) REVERT: E 8 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6789 (pt0) REVERT: E 63 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7388 (mt-10) REVERT: E 123 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7364 (mm-30) REVERT: E 164 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7641 (mmt-90) REVERT: E 328 MET cc_start: 0.8528 (mtm) cc_final: 0.8152 (tmm) REVERT: E 372 LEU cc_start: 0.6006 (tp) cc_final: 0.5742 (tp) outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.0909 time to fit residues: 16.4494 Evaluate side-chains 95 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.113798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.095346 restraints weight = 46535.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.095908 restraints weight = 38829.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.096535 restraints weight = 34964.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.097164 restraints weight = 27515.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.097355 restraints weight = 25162.533| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10892 Z= 0.204 Angle : 0.720 9.020 14954 Z= 0.380 Chirality : 0.049 0.314 1724 Planarity : 0.004 0.046 1681 Dihedral : 22.281 172.988 1931 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.21 % Favored : 87.70 % Rotamer: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.23), residues: 1171 helix: -0.64 (0.29), residues: 303 sheet: -1.69 (0.30), residues: 311 loop : -2.98 (0.23), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 36 TYR 0.024 0.002 TYR C 59 PHE 0.022 0.002 PHE C 228 TRP 0.018 0.002 TRP E 50 HIS 0.006 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (10891) covalent geometry : angle 0.72015 / 0.38 (14954) hydrogen bonds : bond 0.05390 / 3.70 ( 388) hydrogen bonds : angle 6.61583 / 4.58 ( 1006) Misc. bond : bond 0.00054 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7403 (mmt180) cc_final: 0.6981 (mmt90) REVERT: B 126 ASN cc_start: 0.6626 (t0) cc_final: 0.6416 (t0) REVERT: B 136 LEU cc_start: 0.7610 (tp) cc_final: 0.7388 (tp) REVERT: B 146 GLU cc_start: 0.6713 (mt-10) cc_final: 0.5824 (tt0) REVERT: B 216 GLU cc_start: 0.4334 (mm-30) cc_final: 0.4103 (mm-30) REVERT: C 44 ILE cc_start: 0.8904 (mt) cc_final: 0.8654 (mm) REVERT: C 65 PHE cc_start: 0.8376 (t80) cc_final: 0.8123 (t80) REVERT: E 8 GLU cc_start: 0.7887 (tm-30) cc_final: 0.6899 (pt0) REVERT: E 63 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7634 (mt-10) REVERT: E 328 MET cc_start: 0.8558 (mtm) cc_final: 0.8150 (tmm) REVERT: E 372 LEU cc_start: 0.6250 (tp) cc_final: 0.5986 (tp) outliers start: 1 outliers final: 0 residues processed: 112 average time/residue: 0.0854 time to fit residues: 13.9954 Evaluate side-chains 83 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 39 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 83 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN E 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.114338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.095883 restraints weight = 46748.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.096604 restraints weight = 40516.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.097188 restraints weight = 35223.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.098003 restraints weight = 26458.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.098224 restraints weight = 23580.024| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10892 Z= 0.176 Angle : 0.691 8.684 14954 Z= 0.366 Chirality : 0.048 0.323 1724 Planarity : 0.004 0.033 1681 Dihedral : 22.328 173.014 1931 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.87 % Favored : 88.04 % Rotamer: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.23), residues: 1171 helix: -0.65 (0.29), residues: 303 sheet: -1.60 (0.31), residues: 304 loop : -3.01 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 9 TYR 0.025 0.002 TYR C 59 PHE 0.026 0.002 PHE E 161 TRP 0.042 0.004 TRP E 50 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (10891) covalent geometry : angle 0.69091 / 0.37 (14954) hydrogen bonds : bond 0.04821 / 3.30 ( 388) hydrogen bonds : angle 6.42437 / 4.44 ( 1006) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7431 (mmt180) cc_final: 0.6979 (mmt90) REVERT: B 126 ASN cc_start: 0.6556 (t0) cc_final: 0.6304 (t0) REVERT: B 216 GLU cc_start: 0.4277 (mm-30) cc_final: 0.4047 (mm-30) REVERT: C 1 MET cc_start: 0.7815 (tpp) cc_final: 0.7533 (tpp) REVERT: C 44 ILE cc_start: 0.8906 (mt) cc_final: 0.8628 (mm) REVERT: C 186 LEU cc_start: 0.8500 (tp) cc_final: 0.8286 (tp) REVERT: E 8 GLU cc_start: 0.7838 (tm-30) cc_final: 0.6878 (pt0) REVERT: E 22 LEU cc_start: 0.7779 (pp) cc_final: 0.7498 (pp) REVERT: E 25 LEU cc_start: 0.9150 (mm) cc_final: 0.8912 (pp) REVERT: E 63 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7593 (mt-10) REVERT: E 123 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7378 (mm-30) REVERT: E 328 MET cc_start: 0.8440 (mtm) cc_final: 0.8136 (tmm) REVERT: E 372 LEU cc_start: 0.6283 (tp) cc_final: 0.5833 (tp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.0787 time to fit residues: 12.9261 Evaluate side-chains 88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 85 optimal weight: 5.9990 chunk 90 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 76 optimal weight: 40.0000 chunk 31 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.115046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.096625 restraints weight = 46691.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.097229 restraints weight = 36873.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.097853 restraints weight = 33747.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.098200 restraints weight = 25628.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.098725 restraints weight = 23799.285| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10892 Z= 0.165 Angle : 0.681 9.502 14954 Z= 0.361 Chirality : 0.048 0.323 1724 Planarity : 0.004 0.034 1681 Dihedral : 22.347 172.569 1931 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.78 % Favored : 88.13 % Rotamer: Outliers : 0.10 % Allowed : 1.74 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.23), residues: 1171 helix: -0.62 (0.29), residues: 299 sheet: -1.60 (0.31), residues: 307 loop : -2.94 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 145 TYR 0.024 0.002 TYR C 59 PHE 0.022 0.002 PHE C 228 TRP 0.034 0.003 TRP E 50 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (10891) covalent geometry : angle 0.68081 / 0.36 (14954) hydrogen bonds : bond 0.04627 / 3.19 ( 388) hydrogen bonds : angle 6.32061 / 4.37 ( 1006) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7512 (mmt180) cc_final: 0.6995 (mmt90) REVERT: B 126 ASN cc_start: 0.6599 (t0) cc_final: 0.6336 (t0) REVERT: B 216 GLU cc_start: 0.4281 (mm-30) cc_final: 0.4052 (mm-30) REVERT: C 1 MET cc_start: 0.7758 (tpp) cc_final: 0.7445 (tpp) REVERT: C 20 ARG cc_start: 0.7753 (mtt-85) cc_final: 0.7423 (mtt-85) REVERT: C 44 ILE cc_start: 0.8778 (mt) cc_final: 0.8498 (mm) REVERT: C 75 MET cc_start: 0.8396 (mmt) cc_final: 0.8034 (tpp) REVERT: C 230 MET cc_start: 0.4456 (mmt) cc_final: 0.4089 (mmt) REVERT: E 8 GLU cc_start: 0.7880 (tm-30) cc_final: 0.6889 (pt0) REVERT: E 22 LEU cc_start: 0.7629 (pp) cc_final: 0.7428 (pp) REVERT: E 63 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 123 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7314 (mm-30) REVERT: E 328 MET cc_start: 0.8445 (mtm) cc_final: 0.8136 (tmm) REVERT: E 372 LEU cc_start: 0.6260 (tp) cc_final: 0.5807 (tp) outliers start: 1 outliers final: 0 residues processed: 115 average time/residue: 0.1003 time to fit residues: 16.4201 Evaluate side-chains 91 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 94 optimal weight: 0.0030 chunk 41 optimal weight: 0.0470 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 overall best weight: 2.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.114038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.095551 restraints weight = 46306.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.096055 restraints weight = 37167.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.096629 restraints weight = 34740.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.097030 restraints weight = 26265.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.097503 restraints weight = 24175.661| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10892 Z= 0.173 Angle : 0.692 9.978 14954 Z= 0.366 Chirality : 0.048 0.322 1724 Planarity : 0.004 0.043 1681 Dihedral : 22.361 172.149 1931 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.04 % Favored : 87.87 % Rotamer: Outliers : 0.10 % Allowed : 1.45 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.23), residues: 1171 helix: -0.63 (0.29), residues: 296 sheet: -1.63 (0.30), residues: 307 loop : -2.99 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.025 0.002 TYR C 59 PHE 0.021 0.002 PHE C 228 TRP 0.034 0.003 TRP E 50 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (10891) covalent geometry : angle 0.69229 / 0.37 (14954) hydrogen bonds : bond 0.04820 / 3.33 ( 388) hydrogen bonds : angle 6.29197 / 4.34 ( 1006) Misc. bond : bond 0.00051 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 107 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7003 (mmt90) REVERT: B 126 ASN cc_start: 0.6663 (t0) cc_final: 0.6379 (t0) REVERT: B 216 GLU cc_start: 0.4492 (mm-30) cc_final: 0.4261 (mm-30) REVERT: C 1 MET cc_start: 0.7667 (tpp) cc_final: 0.7322 (tpp) REVERT: C 44 ILE cc_start: 0.8813 (mt) cc_final: 0.8549 (mm) REVERT: C 230 MET cc_start: 0.4373 (mmt) cc_final: 0.4018 (mmt) REVERT: E 8 GLU cc_start: 0.7873 (tm-30) cc_final: 0.6913 (pt0) REVERT: E 63 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7423 (mt-10) REVERT: E 123 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7368 (mm-30) REVERT: E 294 ASP cc_start: 0.8606 (m-30) cc_final: 0.8209 (p0) REVERT: E 328 MET cc_start: 0.8455 (mtm) cc_final: 0.8129 (tmm) REVERT: E 372 LEU cc_start: 0.6067 (tp) cc_final: 0.5659 (tp) outliers start: 1 outliers final: 0 residues processed: 108 average time/residue: 0.0881 time to fit residues: 13.7932 Evaluate side-chains 84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.0470 chunk 77 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.116128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.097954 restraints weight = 46285.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.099319 restraints weight = 35538.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.099774 restraints weight = 28631.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.100105 restraints weight = 22039.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.100293 restraints weight = 21357.341| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10892 Z= 0.129 Angle : 0.657 9.183 14954 Z= 0.349 Chirality : 0.048 0.337 1724 Planarity : 0.004 0.039 1681 Dihedral : 22.337 172.675 1931 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.74 % Favored : 90.18 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.23), residues: 1171 helix: -0.45 (0.30), residues: 297 sheet: -1.56 (0.31), residues: 306 loop : -2.92 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 20 TYR 0.021 0.001 TYR C 59 PHE 0.024 0.001 PHE C 228 TRP 0.022 0.003 TRP E 50 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (10891) covalent geometry : angle 0.65661 / 0.35 (14954) hydrogen bonds : bond 0.03846 / 2.64 ( 388) hydrogen bonds : angle 5.97731 / 4.14 ( 1006) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7164 (mmp) cc_final: 0.6809 (tpp) REVERT: B 36 ARG cc_start: 0.7355 (mmt180) cc_final: 0.6838 (mmt90) REVERT: B 126 ASN cc_start: 0.6427 (t0) cc_final: 0.6165 (t0) REVERT: B 216 GLU cc_start: 0.4192 (mm-30) cc_final: 0.3961 (mm-30) REVERT: C 1 MET cc_start: 0.7742 (tpp) cc_final: 0.7340 (tpp) REVERT: C 44 ILE cc_start: 0.8844 (mt) cc_final: 0.8552 (mm) REVERT: C 79 LYS cc_start: 0.7950 (mttt) cc_final: 0.7630 (mmtt) REVERT: C 186 LEU cc_start: 0.8471 (tp) cc_final: 0.8251 (tp) REVERT: E 8 GLU cc_start: 0.7772 (tm-30) cc_final: 0.6823 (pt0) REVERT: E 25 LEU cc_start: 0.9097 (mm) cc_final: 0.8893 (pp) REVERT: E 63 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7296 (mt-10) REVERT: E 123 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7370 (mm-30) REVERT: E 328 MET cc_start: 0.8448 (mtm) cc_final: 0.8106 (tmm) REVERT: E 372 LEU cc_start: 0.6046 (tp) cc_final: 0.5773 (tp) outliers start: 1 outliers final: 0 residues processed: 110 average time/residue: 0.0882 time to fit residues: 14.3541 Evaluate side-chains 88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 111 optimal weight: 0.0270 chunk 116 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 overall best weight: 1.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 HIS C 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.115580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.097352 restraints weight = 46115.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.098162 restraints weight = 39027.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.098720 restraints weight = 33106.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.099560 restraints weight = 25199.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.099767 restraints weight = 22400.544| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10892 Z= 0.142 Angle : 0.658 9.294 14954 Z= 0.348 Chirality : 0.048 0.418 1724 Planarity : 0.004 0.040 1681 Dihedral : 22.334 172.576 1931 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.42 % Favored : 89.50 % Rotamer: Outliers : 0.10 % Allowed : 0.58 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.79 (0.24), residues: 1171 helix: -0.47 (0.30), residues: 298 sheet: -1.53 (0.31), residues: 301 loop : -2.83 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 20 TYR 0.022 0.001 TYR C 59 PHE 0.026 0.002 PHE C 228 TRP 0.027 0.002 TRP E 50 HIS 0.007 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (10891) covalent geometry : angle 0.65785 / 0.35 (14954) hydrogen bonds : bond 0.04195 / 2.88 ( 388) hydrogen bonds : angle 5.95102 / 4.13 ( 1006) Misc. bond : bond 0.00045 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 MET cc_start: 0.7237 (mmp) cc_final: 0.6892 (tpp) REVERT: B 36 ARG cc_start: 0.7367 (mmt180) cc_final: 0.6837 (mmt90) REVERT: B 126 ASN cc_start: 0.6453 (t0) cc_final: 0.6189 (t0) REVERT: B 216 GLU cc_start: 0.4221 (mm-30) cc_final: 0.3985 (mm-30) REVERT: C 1 MET cc_start: 0.7695 (tpp) cc_final: 0.7300 (tpp) REVERT: C 44 ILE cc_start: 0.8845 (mt) cc_final: 0.8543 (mm) REVERT: C 75 MET cc_start: 0.8091 (mmt) cc_final: 0.7390 (tpp) REVERT: C 186 LEU cc_start: 0.8519 (tp) cc_final: 0.8318 (tp) REVERT: C 230 MET cc_start: 0.4333 (mmt) cc_final: 0.4042 (mmt) REVERT: E 8 GLU cc_start: 0.7796 (tm-30) cc_final: 0.6847 (pt0) REVERT: E 63 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 123 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7401 (mm-30) REVERT: E 251 MET cc_start: 0.5693 (tmm) cc_final: 0.5412 (tmm) REVERT: E 328 MET cc_start: 0.8448 (mtm) cc_final: 0.8116 (tmm) REVERT: E 372 LEU cc_start: 0.6066 (tp) cc_final: 0.5657 (tp) outliers start: 1 outliers final: 1 residues processed: 107 average time/residue: 0.0951 time to fit residues: 15.0630 Evaluate side-chains 88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 21 optimal weight: 0.0050 chunk 43 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 107 optimal weight: 0.0270 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 0.1980 overall best weight: 2.8456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.113896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.095666 restraints weight = 46354.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096523 restraints weight = 40514.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.097047 restraints weight = 33842.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.097894 restraints weight = 25686.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.098082 restraints weight = 22629.783| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10892 Z= 0.185 Angle : 0.702 9.525 14954 Z= 0.369 Chirality : 0.049 0.319 1724 Planarity : 0.004 0.082 1681 Dihedral : 22.360 172.167 1931 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.96 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.23), residues: 1171 helix: -0.63 (0.29), residues: 296 sheet: -1.61 (0.31), residues: 306 loop : -2.97 (0.23), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 9 TYR 0.026 0.002 TYR C 59 PHE 0.039 0.002 PHE C 228 TRP 0.031 0.003 TRP E 50 HIS 0.010 0.002 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (10891) covalent geometry : angle 0.70153 / 0.37 (14954) hydrogen bonds : bond 0.04847 / 3.33 ( 388) hydrogen bonds : angle 6.15927 / 4.26 ( 1006) Misc. bond : bond 0.00048 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1357.49 seconds wall clock time: 24 minutes 26.63 seconds (1466.63 seconds total)