Starting phenix.real_space_refine on Thu Jul 2 08:21:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.map" model { file = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ejc_31158/07_2026/7ejc_31158.cif" } resolution = 2.97 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= 0.012 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: 7 Type Number sf(0) Gaussians Br 6 7.06 5 P 18 5.49 5 Mg 3 5.21 5 S 42 5.16 5 C 4644 2.51 5 N 1302 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 7485 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2375 Classifications: {'peptide': 310} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'J46': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 91 Unusual residues: {' MG': 1, 'ANP': 2, 'J46': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {' MG': 1, 'ANP': 1, 'J46': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.90, per 1000 atoms: 0.25 Number of scatterers: 7485 At special positions: 0 Unit cell: (107.97, 70.8, 110.625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 6 34.99 S 42 16.00 P 18 15.00 Mg 3 11.99 O 1470 8.00 N 1302 7.00 C 4644 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 432.1 milliseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 3 sheets defined 49.8% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.577A pdb=" N VAL A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.824A pdb=" N VAL A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 62 removed outlier: 3.718A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 82 removed outlier: 3.754A pdb=" N ASP A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 98 removed outlier: 3.774A pdb=" N PHE A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 134 through 144 removed outlier: 3.720A pdb=" N HIS A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 179 removed outlier: 3.947A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 187 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.003A pdb=" N THR A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 232 removed outlier: 3.672A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 289 through 296 Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.579A pdb=" N VAL C 38 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.823A pdb=" N VAL C 52 " --> pdb=" O THR C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 removed outlier: 3.717A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 82 removed outlier: 3.754A pdb=" N ASP C 72 " --> pdb=" O GLU C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.565A pdb=" N ARG C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 113 Processing helix chain 'C' and resid 134 through 144 removed outlier: 3.693A pdb=" N HIS C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.947A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 196 through 214 removed outlier: 4.003A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.671A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'B' and resid 34 through 45 removed outlier: 3.578A pdb=" N VAL B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.823A pdb=" N VAL B 52 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.718A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 82 removed outlier: 3.754A pdb=" N ASP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 3.565A pdb=" N ARG B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 113 Processing helix chain 'B' and resid 134 through 144 removed outlier: 3.680A pdb=" N VAL B 142 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.946A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 196 through 214 removed outlier: 4.003A pdb=" N THR B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 232 removed outlier: 3.671A pdb=" N ARG B 229 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N THR B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 289 through 296 Processing sheet with id=AA1, first strand: chain 'A' and resid 333 through 334 removed outlier: 3.565A pdb=" N GLY A 333 " --> pdb=" O ASN A 330 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 311 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE A 122 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 300 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU A 124 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU A 302 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LYS A 304 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N LYS A 156 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU A 218 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.495A pdb=" N LYS B 156 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 218 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 122 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LYS B 304 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 311 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY B 333 " --> pdb=" O ASN B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 193 removed outlier: 5.494A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE C 122 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU C 300 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU C 124 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU C 302 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE C 126 " --> pdb=" O LEU C 302 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LYS C 304 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE C 311 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY C 333 " --> pdb=" O ASN C 330 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 999 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: 1.16 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2496 1.34 - 1.48: 1724 1.48 - 1.61: 3312 1.61 - 1.74: 9 1.74 - 1.87: 72 Bond restraints: 7613 Sorted by residual: bond pdb=" O3A ANP B 401 " pdb=" PB ANP B 401 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" O3A ANP C 403 " pdb=" PB ANP C 403 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C04 J46 C 404 " pdb=" C07 J46 C 404 " ideal model delta sigma weight residual 1.391 1.529 -0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" C04 J46 A 602 " pdb=" C07 J46 A 602 " ideal model delta sigma weight residual 1.391 1.529 -0.138 2.00e-02 2.50e+03 4.73e+01 ... (remaining 7608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 10179 3.94 - 7.88: 122 7.88 - 11.83: 18 11.83 - 15.77: 0 15.77 - 19.71: 6 Bond angle restraints: 10325 Sorted by residual: angle pdb=" O01 J46 A 602 " pdb=" S01 J46 A 602 " pdb=" O02 J46 A 602 " ideal model delta sigma weight residual 119.86 100.15 19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" O01 J46 B 403 " pdb=" S01 J46 B 403 " pdb=" O02 J46 B 403 " ideal model delta sigma weight residual 119.86 100.18 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" O01 J46 C 404 " pdb=" S01 J46 C 404 " pdb=" O02 J46 C 404 " ideal model delta sigma weight residual 119.86 100.18 19.68 3.00e+00 1.11e-01 4.30e+01 angle pdb=" N GLY C 236 " pdb=" CA GLY C 236 " pdb=" C GLY C 236 " ideal model delta sigma weight residual 114.69 107.61 7.08 1.19e+00 7.06e-01 3.54e+01 angle pdb=" N GLY B 236 " pdb=" CA GLY B 236 " pdb=" C GLY B 236 " ideal model delta sigma weight residual 114.69 107.67 7.02 1.19e+00 7.06e-01 3.48e+01 ... (remaining 10320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 4256 24.42 - 48.85: 258 48.85 - 73.27: 34 73.27 - 97.69: 3 97.69 - 122.12: 3 Dihedral angle restraints: 4554 sinusoidal: 1902 harmonic: 2652 Sorted by residual: dihedral pdb=" CA ASN A 188 " pdb=" C ASN A 188 " pdb=" N VAL A 189 " pdb=" CA VAL A 189 " ideal model delta harmonic sigma weight residual -180.00 -156.79 -23.21 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASN C 188 " pdb=" C ASN C 188 " pdb=" N VAL C 189 " pdb=" CA VAL C 189 " ideal model delta harmonic sigma weight residual 180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASN B 188 " pdb=" C ASN B 188 " pdb=" N VAL B 189 " pdb=" CA VAL B 189 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 4551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 946 0.059 - 0.119: 184 0.119 - 0.178: 28 0.178 - 0.238: 3 0.238 - 0.297: 3 Chirality restraints: 1164 Sorted by residual: chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ANP B 401 " pdb=" C2' ANP B 401 " pdb=" C4' ANP B 401 " pdb=" O3' ANP B 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C3' ANP C 403 " pdb=" C2' ANP C 403 " pdb=" C4' ANP C 403 " pdb=" O3' ANP C 403 " both_signs ideal model delta sigma weight residual False -2.36 -2.65 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 1161 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 58 " -0.012 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" C LYS B 58 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 58 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU B 59 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 58 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LYS A 58 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS A 58 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 59 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 285 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO C 286 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " 0.028 5.00e-02 4.00e+02 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 21 2.27 - 2.93: 3254 2.93 - 3.59: 10653 3.59 - 4.24: 17973 4.24 - 4.90: 30452 Nonbonded interactions: 62353 Sorted by model distance: nonbonded pdb=" OG1 THR A 134 " pdb="MG MG A 601 " model vdw 1.616 2.170 nonbonded pdb=" OG1 THR C 134 " pdb="MG MG C 402 " model vdw 1.617 2.170 nonbonded pdb=" OG1 THR B 134 " pdb=" OD2 ASP B 222 " model vdw 1.862 3.040 nonbonded pdb=" OG1 THR C 134 " pdb=" O2B ANP C 401 " model vdw 1.896 3.040 nonbonded pdb=" OG1 THR A 134 " pdb=" O2B ANP B 401 " model vdw 1.946 3.040 ... (remaining 62348 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 338) selection = (chain 'B' and resid 22 through 338) selection = (chain 'C' and resid 22 through 338) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.420 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.780 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.011 0.144 7615 Z= 0.554 Angle : 1.191 19.709 10325 Z= 0.688 Chirality : 0.050 0.297 1164 Planarity : 0.004 0.051 1290 Dihedral : 15.456 122.115 2856 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 4.17 % Allowed : 5.38 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -3.39 (0.22), residues: 918 helix: -2.04 (0.20), residues: 417 sheet: -1.38 (0.36), residues: 168 loop : -2.77 (0.26), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 193 TYR 0.020 0.002 TYR B 315 PHE 0.006 0.001 PHE B 126 HIS 0.003 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.01073 / 0.55 ( 7613) covalent geometry : angle 1.19068 / 0.69 (10325) hydrogen bonds : bond 0.15151 / 13.10 ( 347) hydrogen bonds : angle 7.20958 / 5.93 ( 999) Misc. bond : bond 0.01997 / 1.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.360 Fit side-chains REVERT: A 34 ASN cc_start: 0.8335 (t0) cc_final: 0.8001 (t0) REVERT: A 163 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7677 (mm-30) REVERT: C 39 LYS cc_start: 0.9129 (mptt) cc_final: 0.8820 (mmtm) REVERT: C 68 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7083 (tm-30) REVERT: C 210 MET cc_start: 0.8817 (mtp) cc_final: 0.8587 (mtp) REVERT: B 68 GLU cc_start: 0.7777 (tm-30) cc_final: 0.6987 (tm-30) REVERT: B 198 ASP cc_start: 0.8725 (m-30) cc_final: 0.8523 (m-30) outliers start: 31 outliers final: 5 residues processed: 128 average time/residue: 0.7422 time to fit residues: 99.3120 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain B residue 134 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 34 ASN A 138 HIS A 242 GLN A 290 ASN A 330 ASN C 30 GLN C 93 HIS C 138 HIS C 242 GLN C 290 ASN C 330 ASN B 30 GLN B 93 HIS B 138 HIS B 242 GLN B 290 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.066702 restraints weight = 13253.098| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.10 r_work: 0.2811 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7615 Z= 0.165 Angle : 0.662 8.114 10325 Z= 0.364 Chirality : 0.042 0.128 1164 Planarity : 0.004 0.046 1290 Dihedral : 11.502 110.401 1168 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.68 % Favored : 94.99 % Rotamer: Outliers : 2.82 % Allowed : 14.11 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -1.63 (0.25), residues: 918 helix: -0.08 (0.26), residues: 393 sheet: -0.62 (0.38), residues: 156 loop : -2.38 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 27 TYR 0.017 0.001 TYR A 315 PHE 0.007 0.001 PHE C 126 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 7613) covalent geometry : angle 0.66216 / 0.36 (10325) hydrogen bonds : bond 0.04881 / 4.23 ( 347) hydrogen bonds : angle 5.47219 / 4.49 ( 999) Misc. bond : bond 0.00328 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 LYS cc_start: 0.9197 (mptt) cc_final: 0.8937 (mmtm) REVERT: B 223 SER cc_start: 0.8662 (m) cc_final: 0.8414 (p) outliers start: 21 outliers final: 10 residues processed: 91 average time/residue: 0.6627 time to fit residues: 63.4272 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 326 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.079071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064379 restraints weight = 13534.735| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.21 r_work: 0.2751 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9188 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7615 Z= 0.179 Angle : 0.637 7.626 10325 Z= 0.350 Chirality : 0.042 0.136 1164 Planarity : 0.004 0.048 1290 Dihedral : 10.798 96.314 1162 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 2.82 % Allowed : 17.74 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % 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: -1.18 (0.27), residues: 918 helix: 0.34 (0.26), residues: 411 sheet: -0.67 (0.40), residues: 165 loop : -2.19 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.019 0.001 TYR B 315 PHE 0.008 0.001 PHE B 92 HIS 0.003 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 7613) covalent geometry : angle 0.63667 / 0.35 (10325) hydrogen bonds : bond 0.04999 / 4.32 ( 347) hydrogen bonds : angle 5.21418 / 4.28 ( 999) Misc. bond : bond 0.00316 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 43 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8598 (mt-10) REVERT: B 68 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7891 (tm-30) outliers start: 21 outliers final: 13 residues processed: 77 average time/residue: 0.6307 time to fit residues: 51.3213 Evaluate side-chains 70 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 8 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 63 optimal weight: 0.0970 chunk 89 optimal weight: 0.0870 chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** 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 = 0.3241 r_free = 0.3241 target = 0.082406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.067921 restraints weight = 13697.292| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.19 r_work: 0.2836 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7615 Z= 0.118 Angle : 0.570 7.301 10325 Z= 0.315 Chirality : 0.041 0.169 1164 Planarity : 0.003 0.047 1290 Dihedral : 10.438 84.004 1162 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.42 % Allowed : 18.55 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.27), residues: 918 helix: 0.59 (0.26), residues: 417 sheet: -0.75 (0.40), residues: 165 loop : -1.90 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.011 0.001 TYR C 315 PHE 0.005 0.001 PHE C 248 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 ( 7613) covalent geometry : angle 0.57003 / 0.31 (10325) hydrogen bonds : bond 0.03757 / 3.26 ( 347) hydrogen bonds : angle 4.79055 / 3.94 ( 999) Misc. bond : bond 0.00204 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8554 (mt-10) REVERT: B 43 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: B 159 TYR cc_start: 0.8870 (t80) cc_final: 0.8510 (t80) REVERT: B 184 ASP cc_start: 0.8952 (m-30) cc_final: 0.8733 (m-30) REVERT: B 223 SER cc_start: 0.8696 (m) cc_final: 0.8365 (p) outliers start: 18 outliers final: 11 residues processed: 78 average time/residue: 0.6045 time to fit residues: 49.9748 Evaluate side-chains 73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 0.0060 chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.2980 chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.8400 ------------------------------------------------------------------------------- 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 = 0.3182 r_free = 0.3182 target = 0.079340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.064613 restraints weight = 13528.828| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.22 r_work: 0.2755 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7615 Z= 0.167 Angle : 0.606 7.460 10325 Z= 0.334 Chirality : 0.042 0.144 1164 Planarity : 0.004 0.038 1290 Dihedral : 10.299 75.048 1161 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.47 % Favored : 95.32 % Rotamer: Outliers : 2.28 % Allowed : 19.49 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.27), residues: 918 helix: 0.68 (0.26), residues: 417 sheet: -0.55 (0.41), residues: 165 loop : -1.79 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.017 0.001 TYR C 315 PHE 0.007 0.001 PHE C 327 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 ( 7613) covalent geometry : angle 0.60584 / 0.33 (10325) hydrogen bonds : bond 0.04551 / 3.98 ( 347) hydrogen bonds : angle 4.91441 / 4.08 ( 999) Misc. bond : bond 0.00329 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 285 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8619 (tttm) REVERT: C 43 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: B 43 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8583 (mt-10) REVERT: B 68 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7940 (tp30) REVERT: B 159 TYR cc_start: 0.8932 (t80) cc_final: 0.8546 (t80) REVERT: B 184 ASP cc_start: 0.9012 (m-30) cc_final: 0.8793 (m-30) outliers start: 17 outliers final: 12 residues processed: 75 average time/residue: 0.6383 time to fit residues: 50.5973 Evaluate side-chains 79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** 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 = 0.3218 r_free = 0.3218 target = 0.081162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.066446 restraints weight = 13506.729| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.22 r_work: 0.2797 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7615 Z= 0.125 Angle : 0.575 7.569 10325 Z= 0.318 Chirality : 0.040 0.124 1164 Planarity : 0.003 0.034 1290 Dihedral : 10.207 69.082 1161 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.55 % Allowed : 21.37 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.28), residues: 918 helix: 0.90 (0.26), residues: 414 sheet: -0.62 (0.41), residues: 165 loop : -1.72 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 27 TYR 0.013 0.001 TYR C 315 PHE 0.005 0.001 PHE C 126 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 7613) covalent geometry : angle 0.57469 / 0.32 (10325) hydrogen bonds : bond 0.03871 / 3.39 ( 347) hydrogen bonds : angle 4.71224 / 3.92 ( 999) Misc. bond : bond 0.00226 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: C 306 ARG cc_start: 0.8194 (mmp-170) cc_final: 0.7978 (mmp-170) REVERT: B 39 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8805 (mmtt) REVERT: B 43 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: B 159 TYR cc_start: 0.8970 (t80) cc_final: 0.8501 (t80) REVERT: B 184 ASP cc_start: 0.9006 (m-30) cc_final: 0.8789 (m-30) REVERT: B 223 SER cc_start: 0.8612 (m) cc_final: 0.8240 (p) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.6290 time to fit residues: 54.4894 Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.081472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.066872 restraints weight = 13505.424| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.19 r_work: 0.2816 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7615 Z= 0.121 Angle : 0.578 7.648 10325 Z= 0.318 Chirality : 0.040 0.126 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.119 65.545 1161 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Rotamer: Outliers : 2.69 % Allowed : 21.37 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.28), residues: 918 helix: 0.95 (0.26), residues: 414 sheet: -0.55 (0.42), residues: 162 loop : -1.62 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.011 0.001 TYR C 315 PHE 0.006 0.001 PHE C 126 HIS 0.001 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 7613) covalent geometry : angle 0.57752 / 0.32 (10325) hydrogen bonds : bond 0.03774 / 3.32 ( 347) hydrogen bonds : angle 4.64600 / 3.88 ( 999) Misc. bond : bond 0.00227 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (mt-10) REVERT: B 43 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8587 (mt-10) REVERT: B 159 TYR cc_start: 0.8946 (t80) cc_final: 0.8561 (t80) REVERT: B 223 SER cc_start: 0.8646 (m) cc_final: 0.8294 (p) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.5027 time to fit residues: 41.5990 Evaluate side-chains 77 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.0980 chunk 33 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.081204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.066572 restraints weight = 13525.882| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.18 r_work: 0.2806 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7615 Z= 0.130 Angle : 0.583 7.533 10325 Z= 0.322 Chirality : 0.040 0.125 1164 Planarity : 0.003 0.030 1290 Dihedral : 10.095 65.114 1161 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.96 % Allowed : 21.64 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.28), residues: 918 helix: 0.91 (0.26), residues: 414 sheet: -0.60 (0.41), residues: 165 loop : -1.52 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.012 0.001 TYR C 315 PHE 0.006 0.001 PHE C 126 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7613) covalent geometry : angle 0.58320 / 0.32 (10325) hydrogen bonds : bond 0.03937 / 3.46 ( 347) hydrogen bonds : angle 4.59478 / 3.86 ( 999) Misc. bond : bond 0.00241 / 0.12 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8529 (mt-10) REVERT: B 43 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: B 159 TYR cc_start: 0.8979 (t80) cc_final: 0.8517 (t80) REVERT: B 223 SER cc_start: 0.8622 (m) cc_final: 0.8261 (p) outliers start: 22 outliers final: 16 residues processed: 73 average time/residue: 0.5648 time to fit residues: 43.6500 Evaluate side-chains 72 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** 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 = 0.3241 r_free = 0.3241 target = 0.082308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067792 restraints weight = 13375.077| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.17 r_work: 0.2833 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7615 Z= 0.117 Angle : 0.575 7.759 10325 Z= 0.317 Chirality : 0.040 0.125 1164 Planarity : 0.003 0.024 1290 Dihedral : 10.058 64.210 1161 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.55 % Allowed : 22.31 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 918 helix: 0.91 (0.26), residues: 414 sheet: -0.57 (0.42), residues: 162 loop : -1.45 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.010 0.001 TYR C 315 PHE 0.005 0.001 PHE C 126 HIS 0.001 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 ( 7613) covalent geometry : angle 0.57497 / 0.32 (10325) hydrogen bonds : bond 0.03694 / 3.26 ( 347) hydrogen bonds : angle 4.51472 / 3.80 ( 999) Misc. bond : bond 0.00207 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: B 43 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: B 159 TYR cc_start: 0.8949 (t80) cc_final: 0.8503 (t80) REVERT: B 223 SER cc_start: 0.8577 (m) cc_final: 0.8212 (p) outliers start: 19 outliers final: 12 residues processed: 75 average time/residue: 0.5234 time to fit residues: 41.8794 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 158 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 71 optimal weight: 0.0050 chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.0040 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.082097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.067509 restraints weight = 13403.765| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.17 r_work: 0.2828 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9135 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7615 Z= 0.122 Angle : 0.595 7.868 10325 Z= 0.325 Chirality : 0.040 0.132 1164 Planarity : 0.003 0.023 1290 Dihedral : 10.007 63.974 1161 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.75 % Allowed : 23.39 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.28), residues: 918 helix: 0.87 (0.26), residues: 420 sheet: -0.28 (0.42), residues: 156 loop : -1.40 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.011 0.001 TYR C 315 PHE 0.006 0.001 PHE C 126 HIS 0.001 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7613) covalent geometry : angle 0.59477 / 0.33 (10325) hydrogen bonds : bond 0.03728 / 3.26 ( 347) hydrogen bonds : angle 4.48478 / 3.77 ( 999) Misc. bond : bond 0.00215 / 0.11 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: B 43 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8567 (mt-10) REVERT: B 159 TYR cc_start: 0.8981 (t80) cc_final: 0.8539 (t80) REVERT: B 223 SER cc_start: 0.8583 (m) cc_final: 0.8211 (p) outliers start: 13 outliers final: 12 residues processed: 68 average time/residue: 0.5654 time to fit residues: 40.8224 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain B residue 34 ASN Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 64 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 88 optimal weight: 0.0060 chunk 66 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8598 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.082140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.067594 restraints weight = 13326.784| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.17 r_work: 0.2823 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9136 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7615 Z= 0.123 Angle : 0.592 9.313 10325 Z= 0.323 Chirality : 0.041 0.151 1164 Planarity : 0.003 0.030 1290 Dihedral : 9.996 64.097 1161 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.88 % Allowed : 23.25 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.28), residues: 918 helix: 0.86 (0.26), residues: 420 sheet: -0.35 (0.41), residues: 159 loop : -1.35 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.011 0.001 TYR C 315 PHE 0.006 0.001 PHE C 126 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 7613) covalent geometry : angle 0.59201 / 0.32 (10325) hydrogen bonds : bond 0.03731 / 3.27 ( 347) hydrogen bonds : angle 4.47336 / 3.76 ( 999) Misc. bond : bond 0.00219 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.18 seconds wall clock time: 42 minutes 58.87 seconds (2578.87 seconds total)