Starting phenix.real_space_refine on Fri Sep 11 05:07:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejc_31158/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejc_31158/09_2026/7ejc_31158.map" } 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-2.2.1-6174/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: 1.49, per 1000 atoms: 0.20 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: 0.49 Conformation dependent library (CDL) restraints added in 370.3 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: 1.21 Time building geometry restraints manager: 0.71 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: 5.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.050 Find NCS groups from input model: 0.150 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:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- 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 1.19086 / 0.69 (10325) hydrogen bonds : bond 0.15151 / 13.17 ( 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 : 0.216 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: 0.6648 time to fit residues: 88.9550 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 : 0.285 ------------------------------------------------------------------------------- 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 290 ASN C 330 ASN B 30 GLN B 93 HIS B 138 HIS ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 290 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.080842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.066436 restraints weight = 13124.261| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.11 r_work: 0.2802 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7615 Z= 0.167 Angle : 0.666 8.276 10325 Z= 0.367 Chirality : 0.042 0.127 1164 Planarity : 0.004 0.046 1290 Dihedral : 11.653 113.513 1168 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 2.96 % Allowed : 14.25 % Favored : 82.80 % 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: -1.66 (0.25), residues: 918 helix: -0.12 (0.26), residues: 393 sheet: -0.62 (0.38), residues: 156 loop : -2.40 (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 0.008 0.001 PHE C 126 HIS 0.003 0.000 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 ( 7613) covalent geometry : angle 0.66633 / 0.37 (10325) hydrogen bonds : bond 0.05022 / 4.36 ( 347) hydrogen bonds : angle 5.56005 / 4.56 ( 999) Misc. bond : bond 0.00344 / 0.17 ( 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 95 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8691 (t0) cc_final: 0.8477 (t0) REVERT: A 39 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8722 (mppt) REVERT: C 39 LYS cc_start: 0.9188 (mptt) cc_final: 0.8932 (mmtm) REVERT: B 223 SER cc_start: 0.8657 (m) cc_final: 0.8416 (p) outliers start: 22 outliers final: 13 residues processed: 91 average time/residue: 0.5878 time to fit residues: 56.1916 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 : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 34 ASN Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain B residue 34 ASN 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 125 MET 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: 4.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 0.0020 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- 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 = 0.3232 r_free = 0.3232 target = 0.081991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.067366 restraints weight = 13532.187| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.21 r_work: 0.2818 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9132 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7615 Z= 0.132 Angle : 0.597 7.351 10325 Z= 0.330 Chirality : 0.041 0.131 1164 Planarity : 0.003 0.040 1290 Dihedral : 10.956 103.265 1162 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 2.82 % Allowed : 16.53 % Favored : 80.65 % 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: -1.09 (0.26), residues: 918 helix: 0.50 (0.27), residues: 393 sheet: -0.81 (0.39), residues: 165 loop : -2.05 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 27 TYR 0.013 0.001 TYR A 315 PHE 0.006 0.001 PHE A 327 HIS 0.002 0.001 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 7613) covalent geometry : angle 0.59659 / 0.33 (10325) hydrogen bonds : bond 0.04277 / 3.73 ( 347) hydrogen bonds : angle 5.06158 / 4.16 ( 999) Misc. bond : bond 0.00256 / 0.13 ( 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 87 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8726 (mtmt) REVERT: C 39 LYS cc_start: 0.9195 (mptt) cc_final: 0.8959 (mmtm) REVERT: C 326 MET cc_start: 0.9073 (ttm) cc_final: 0.8816 (ttp) REVERT: B 43 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8608 (mt-10) REVERT: B 223 SER cc_start: 0.8675 (m) cc_final: 0.8336 (p) outliers start: 21 outliers final: 14 residues processed: 78 average time/residue: 0.5728 time to fit residues: 47.2252 Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU 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 C residue 223 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 99 ILE 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: 0.0040 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 33 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3248 r_free = 0.3248 target = 0.082724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.068143 restraints weight = 13794.809| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.21 r_work: 0.2841 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9123 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7615 Z= 0.121 Angle : 0.566 7.388 10325 Z= 0.311 Chirality : 0.040 0.127 1164 Planarity : 0.003 0.055 1290 Dihedral : 10.355 83.882 1162 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.82 % Allowed : 18.28 % Favored : 78.90 % 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: 0.58 (0.26), residues: 417 sheet: -0.79 (0.40), residues: 165 loop : -1.86 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 27 TYR 0.011 0.001 TYR B 315 PHE 0.006 0.001 PHE C 327 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 7613) covalent geometry : angle 0.56556 / 0.31 (10325) hydrogen bonds : bond 0.03881 / 3.34 ( 347) hydrogen bonds : angle 4.72098 / 3.88 ( 999) Misc. bond : bond 0.00228 / 0.11 ( 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 91 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8492 (mt-10) REVERT: C 39 LYS cc_start: 0.9215 (mptt) cc_final: 0.8972 (mmtm) REVERT: C 326 MET cc_start: 0.9029 (ttm) cc_final: 0.8801 (ttp) REVERT: B 43 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: B 68 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8068 (tp30) REVERT: B 159 TYR cc_start: 0.8892 (t80) cc_final: 0.8480 (t80) REVERT: B 223 SER cc_start: 0.8569 (m) cc_final: 0.8254 (p) outliers start: 21 outliers final: 11 residues processed: 84 average time/residue: 0.5437 time to fit residues: 48.3110 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 : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU 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 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 Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 39 optimal weight: 0.0040 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 83 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.081681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.067089 restraints weight = 13658.889| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.20 r_work: 0.2815 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7615 Z= 0.131 Angle : 0.572 7.491 10325 Z= 0.316 Chirality : 0.041 0.172 1164 Planarity : 0.003 0.036 1290 Dihedral : 10.225 75.351 1161 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % Rotamer: Outliers : 2.69 % Allowed : 19.62 % Favored : 77.69 % 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: -0.69 (0.27), residues: 918 helix: 0.67 (0.26), residues: 417 sheet: -0.64 (0.41), residues: 165 loop : -1.76 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.013 0.001 TYR C 315 PHE 0.006 0.001 PHE B 92 HIS 0.002 0.001 HIS A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 7613) covalent geometry : angle 0.57238 / 0.32 (10325) hydrogen bonds : bond 0.04031 / 3.53 ( 347) hydrogen bonds : angle 4.70777 / 3.92 ( 999) Misc. bond : bond 0.00253 / 0.13 ( 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 87 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.253 Fit side-chains REVERT: A 39 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8752 (mmtm) REVERT: A 43 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: C 39 LYS cc_start: 0.9241 (mptt) cc_final: 0.8904 (mmtm) REVERT: C 43 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: B 43 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8570 (mt-10) REVERT: B 68 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8005 (tp30) REVERT: B 159 TYR cc_start: 0.8909 (t80) cc_final: 0.8558 (t80) REVERT: B 184 ASP cc_start: 0.8979 (m-30) cc_final: 0.8777 (p0) REVERT: B 223 SER cc_start: 0.8610 (m) cc_final: 0.8275 (p) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.5656 time to fit residues: 47.9066 Evaluate side-chains 79 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU 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 34 ASN 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 125 MET 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: 0.9980 chunk 17 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.080185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.065389 restraints weight = 13611.971| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.22 r_work: 0.2780 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9170 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7615 Z= 0.153 Angle : 0.591 7.569 10325 Z= 0.326 Chirality : 0.042 0.139 1164 Planarity : 0.003 0.036 1290 Dihedral : 10.197 69.627 1161 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.88 % Rotamer: Outliers : 2.28 % Allowed : 20.43 % Favored : 77.28 % 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: -0.57 (0.28), residues: 918 helix: 0.77 (0.26), residues: 414 sheet: -0.54 (0.41), residues: 165 loop : -1.71 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 27 TYR 0.016 0.001 TYR C 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 0.00331 / 0.15 ( 7613) covalent geometry : angle 0.59129 / 0.33 (10325) hydrogen bonds : bond 0.04301 / 3.83 ( 347) hydrogen bonds : angle 4.77066 / 4.00 ( 999) Misc. bond : bond 0.00295 / 0.15 ( 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 83 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8717 (mppt) REVERT: A 43 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8514 (mt-10) REVERT: A 285 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8643 (tttm) REVERT: C 39 LYS cc_start: 0.9251 (mptt) cc_final: 0.8958 (mmtp) REVERT: C 43 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: B 43 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: B 68 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8039 (tp30) REVERT: B 159 TYR cc_start: 0.8978 (t80) cc_final: 0.8482 (t80) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.6013 time to fit residues: 47.5997 Evaluate side-chains 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 34 ASN 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 158 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 19 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.081421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.066694 restraints weight = 13523.933| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.23 r_work: 0.2809 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.3058 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= 0.123 Angle : 0.568 7.516 10325 Z= 0.314 Chirality : 0.041 0.126 1164 Planarity : 0.003 0.032 1290 Dihedral : 10.126 65.594 1161 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.82 % Allowed : 20.70 % Favored : 76.48 % 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: -0.48 (0.28), residues: 918 helix: 0.85 (0.26), residues: 414 sheet: -0.59 (0.41), residues: 165 loop : -1.59 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 306 TYR 0.012 0.001 TYR C 315 PHE 0.005 0.001 PHE B 92 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7613) covalent geometry : angle 0.56807 / 0.31 (10325) hydrogen bonds : bond 0.03871 / 3.45 ( 347) hydrogen bonds : angle 4.63980 / 3.91 ( 999) Misc. bond : bond 0.00228 / 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 84 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: C 43 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: B 43 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: B 68 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8018 (tp30) REVERT: B 159 TYR cc_start: 0.8983 (t80) cc_final: 0.8548 (t80) REVERT: B 184 ASP cc_start: 0.9007 (m-30) cc_final: 0.8792 (p0) REVERT: B 223 SER cc_start: 0.8626 (m) cc_final: 0.8256 (p) outliers start: 21 outliers final: 14 residues processed: 76 average time/residue: 0.5576 time to fit residues: 44.7002 Evaluate side-chains 77 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 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 72 ASP Chi-restraints excluded: chain B residue 125 MET 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: 0.8980 chunk 23 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3206 r_free = 0.3206 target = 0.080531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.065822 restraints weight = 13575.916| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.20 r_work: 0.2792 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7615 Z= 0.142 Angle : 0.582 7.629 10325 Z= 0.320 Chirality : 0.041 0.139 1164 Planarity : 0.003 0.032 1290 Dihedral : 10.098 65.733 1161 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.44 % 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: -0.42 (0.28), residues: 918 helix: 0.87 (0.26), residues: 414 sheet: -0.56 (0.41), residues: 165 loop : -1.54 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.013 0.001 TYR C 315 PHE 0.006 0.001 PHE C 126 HIS 0.002 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 7613) covalent geometry : angle 0.58177 / 0.32 (10325) hydrogen bonds : bond 0.04085 / 3.62 ( 347) hydrogen bonds : angle 4.68745 / 3.95 ( 999) Misc. bond : bond 0.00272 / 0.14 ( 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: 19 poor density : 62 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8798 (mmtp) REVERT: A 43 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8537 (mt-10) REVERT: C 43 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8555 (mt-10) REVERT: B 43 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: B 68 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8028 (tp30) REVERT: B 159 TYR cc_start: 0.8991 (t80) cc_final: 0.8543 (t80) outliers start: 19 outliers final: 15 residues processed: 74 average time/residue: 0.6096 time to fit residues: 47.4868 Evaluate side-chains 77 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU 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 72 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 125 MET 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: 6.9990 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 0.0060 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 87 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3244 r_free = 0.3244 target = 0.082507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.067945 restraints weight = 13339.687| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.18 r_work: 0.2837 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7615 Z= 0.115 Angle : 0.569 7.581 10325 Z= 0.313 Chirality : 0.040 0.144 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.052 64.038 1161 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % 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: -0.32 (0.28), residues: 918 helix: 0.84 (0.26), residues: 420 sheet: -0.39 (0.42), residues: 159 loop : -1.40 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 306 TYR 0.010 0.001 TYR C 315 PHE 0.005 0.001 PHE B 92 HIS 0.002 0.000 HIS B 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 7613) covalent geometry : angle 0.56898 / 0.31 (10325) hydrogen bonds : bond 0.03602 / 3.20 ( 347) hydrogen bonds : angle 4.52722 / 3.82 ( 999) Misc. bond : bond 0.00197 / 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 83 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8792 (mmtm) REVERT: A 43 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: C 43 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: B 43 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8563 (mt-10) REVERT: B 159 TYR cc_start: 0.8971 (t80) cc_final: 0.8489 (t80) REVERT: B 223 SER cc_start: 0.8583 (m) cc_final: 0.8216 (p) outliers start: 20 outliers final: 14 residues processed: 76 average time/residue: 0.5525 time to fit residues: 44.3677 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 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 72 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 125 MET 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: 0.5980 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3233 r_free = 0.3233 target = 0.081928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.067184 restraints weight = 13439.178| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.22 r_work: 0.2816 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 moved from start: 0.3295 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 : 0.580 7.683 10325 Z= 0.317 Chirality : 0.041 0.148 1164 Planarity : 0.003 0.031 1290 Dihedral : 10.008 63.664 1161 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Rotamer: Outliers : 2.42 % Allowed : 22.18 % 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: -0.26 (0.28), residues: 918 helix: 0.87 (0.26), residues: 420 sheet: -0.38 (0.42), residues: 159 loop : -1.33 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 A 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 7613) covalent geometry : angle 0.57955 / 0.32 (10325) hydrogen bonds : bond 0.03768 / 3.30 ( 347) hydrogen bonds : angle 4.49812 / 3.79 ( 999) Misc. bond : bond 0.00224 / 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 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: C 43 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: B 43 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: B 159 TYR cc_start: 0.8914 (t80) cc_final: 0.8444 (t80) REVERT: B 223 SER cc_start: 0.8607 (m) cc_final: 0.8202 (p) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.5647 time to fit residues: 39.9502 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 77 GLU 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 72 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 125 MET 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 64 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.078577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.063904 restraints weight = 13270.018| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.15 r_work: 0.2738 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9202 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7615 Z= 0.186 Angle : 0.633 7.724 10325 Z= 0.347 Chirality : 0.043 0.144 1164 Planarity : 0.004 0.037 1290 Dihedral : 10.209 70.159 1161 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.34 % Favored : 94.34 % 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: -0.29 (0.28), residues: 918 helix: 0.90 (0.26), residues: 414 sheet: -0.41 (0.42), residues: 165 loop : -1.40 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 27 TYR 0.019 0.001 TYR A 315 PHE 0.007 0.001 PHE A 327 HIS 0.003 0.001 HIS C 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 7613) covalent geometry : angle 0.63253 / 0.35 (10325) hydrogen bonds : bond 0.04886 / 4.28 ( 347) hydrogen bonds : angle 4.89113 / 4.13 ( 999) Misc. bond : bond 0.00348 / 0.17 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2109.18 seconds wall clock time: 36 minutes 50.44 seconds (2210.44 seconds total)