Starting phenix.real_space_refine on Wed Feb 12 11:46:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ejc_31158/02_2025/7ejc_31158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejc_31158/02_2025/7ejc_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_31158/02_2025/7ejc_31158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejc_31158/02_2025/7ejc_31158.map" model { file = "/net/cci-nas-00/data/ceres_data/7ejc_31158/02_2025/7ejc_31158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejc_31158/02_2025/7ejc_31158.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.83, per 1000 atoms: 0.78 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: 2.03 Conformation dependent library (CDL) restraints added in 981.0 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: 0.88 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: 2.16 Time building geometry restraints manager: 2.15 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: 4283 24.42 - 48.85: 312 48.85 - 73.27: 34 73.27 - 97.69: 6 97.69 - 122.12: 3 Dihedral angle restraints: 4638 sinusoidal: 1986 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 4635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 950 0.059 - 0.119: 180 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: 2.830 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.350 Find NCS groups from input model: 0.260 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:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 7613 Z= 0.724 Angle : 1.183 19.709 10325 Z= 0.662 Chirality : 0.049 0.297 1164 Planarity : 0.004 0.051 1290 Dihedral : 16.421 122.115 2940 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 11.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS B 294 PHE 0.006 0.001 PHE B 126 TYR 0.020 0.002 TYR B 315 ARG 0.006 0.001 ARG B 193 *********************** 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 : 0.845 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 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: 0.8588 (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: 1.5588 time to fit residues: 208.2882 Evaluate side-chains 67 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 79 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 34 ASN A 138 HIS ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 290 ASN A 330 ASN C 30 GLN C 93 HIS C 138 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C 330 ASN B 30 GLN B 93 HIS B 138 HIS ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN B 330 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.068893 restraints weight = 13260.671| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.12 r_work: 0.2857 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7613 Z= 0.187 Angle : 0.611 7.252 10325 Z= 0.337 Chirality : 0.041 0.128 1164 Planarity : 0.004 0.039 1290 Dihedral : 12.386 93.214 1252 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.82 % Allowed : 14.92 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.25), residues: 918 helix: -0.06 (0.26), residues: 393 sheet: -0.95 (0.37), residues: 156 loop : -2.27 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 294 PHE 0.007 0.001 PHE A 248 TYR 0.013 0.001 TYR A 315 ARG 0.008 0.001 ARG C 27 *********************** 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 101 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 326 MET cc_start: 0.8986 (ttm) cc_final: 0.8777 (ttp) REVERT: B 43 GLU cc_start: 0.8816 (mp0) cc_final: 0.8595 (mt-10) REVERT: B 159 TYR cc_start: 0.8957 (t80) cc_final: 0.8493 (t80) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 1.4264 time to fit residues: 144.9914 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 : 0.893 ------------------------------------------------------------------------------- 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 158 MET Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 142 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 91 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.080826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.066043 restraints weight = 13889.014| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.26 r_work: 0.2785 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9006 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7613 Z= 0.204 Angle : 0.592 7.422 10325 Z= 0.327 Chirality : 0.041 0.131 1164 Planarity : 0.004 0.038 1290 Dihedral : 11.017 61.066 1248 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.58 % Favored : 95.21 % Rotamer: Outliers : 2.82 % Allowed : 16.94 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.27), residues: 918 helix: 0.41 (0.26), residues: 411 sheet: -0.94 (0.38), residues: 165 loop : -2.14 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 294 PHE 0.007 0.001 PHE C 126 TYR 0.015 0.001 TYR C 315 ARG 0.005 0.000 ARG B 193 *********************** 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 91 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8677 (mtmt) REVERT: A 43 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: C 39 LYS cc_start: 0.9204 (mppt) cc_final: 0.8834 (mmtm) REVERT: B 43 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: B 159 TYR cc_start: 0.9041 (t80) cc_final: 0.8458 (t80) REVERT: B 184 ASP cc_start: 0.8990 (m-30) cc_final: 0.8770 (m-30) outliers start: 21 outliers final: 10 residues processed: 83 average time/residue: 1.2993 time to fit residues: 114.3438 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 97 SER Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain C residue 34 ASN 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 B residue 43 GLU Chi-restraints excluded: chain B residue 97 SER 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 13 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.067703 restraints weight = 13529.543| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.21 r_work: 0.2831 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7613 Z= 0.166 Angle : 0.559 7.528 10325 Z= 0.309 Chirality : 0.040 0.162 1164 Planarity : 0.003 0.033 1290 Dihedral : 10.626 56.935 1245 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.15 % Allowed : 18.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.27), residues: 918 helix: 0.76 (0.26), residues: 411 sheet: -0.80 (0.39), residues: 165 loop : -1.87 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 294 PHE 0.006 0.001 PHE C 126 TYR 0.011 0.001 TYR C 315 ARG 0.004 0.000 ARG B 27 *********************** 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 90 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8652 (mtmt) REVERT: A 43 GLU cc_start: 0.8806 (mp0) cc_final: 0.8512 (mt-10) REVERT: C 43 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8531 (mt-10) REVERT: B 43 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.8579 (mt-10) REVERT: B 184 ASP cc_start: 0.8970 (m-30) cc_final: 0.8686 (p0) REVERT: B 223 SER cc_start: 0.8589 (m) cc_final: 0.8193 (p) outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 1.1586 time to fit residues: 104.9819 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain C residue 34 ASN 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 38 VAL Chi-restraints excluded: chain B residue 43 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 91 optimal weight: 0.0870 chunk 76 optimal weight: 7.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3253 r_free = 0.3253 target = 0.083121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.068442 restraints weight = 13392.936| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.23 r_work: 0.2849 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7613 Z= 0.150 Angle : 0.542 7.625 10325 Z= 0.300 Chirality : 0.040 0.128 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.410 55.474 1245 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.34 % Allowed : 19.49 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 918 helix: 0.92 (0.27), residues: 408 sheet: -0.62 (0.41), residues: 165 loop : -1.68 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 294 PHE 0.006 0.001 PHE C 126 TYR 0.010 0.001 TYR B 315 ARG 0.003 0.000 ARG B 27 *********************** 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 88 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8834 (mp0) cc_final: 0.8514 (mt-10) REVERT: C 43 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: B 39 LYS cc_start: 0.9086 (mmtm) cc_final: 0.8886 (mppt) REVERT: B 43 GLU cc_start: 0.8855 (mp0) cc_final: 0.8589 (mt-10) REVERT: B 72 ASP cc_start: 0.8568 (p0) cc_final: 0.8313 (m-30) REVERT: B 223 SER cc_start: 0.8514 (m) cc_final: 0.8128 (p) outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 1.3011 time to fit residues: 118.3986 Evaluate side-chains 72 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 65 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET 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 B residue 38 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 77 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN B 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.082756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.068042 restraints weight = 13392.372| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.23 r_work: 0.2835 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7613 Z= 0.157 Angle : 0.551 7.697 10325 Z= 0.305 Chirality : 0.040 0.125 1164 Planarity : 0.003 0.044 1290 Dihedral : 10.343 56.180 1245 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.61 % Allowed : 20.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.28), residues: 918 helix: 0.84 (0.26), residues: 420 sheet: -0.28 (0.42), residues: 159 loop : -1.51 (0.31), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 294 PHE 0.005 0.001 PHE C 327 TYR 0.011 0.001 TYR C 315 ARG 0.011 0.000 ARG B 27 *********************** 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 81 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8518 (mt-10) REVERT: C 39 LYS cc_start: 0.9224 (mppt) cc_final: 0.8792 (mmtm) REVERT: C 43 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: B 39 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8834 (mmtt) REVERT: B 43 GLU cc_start: 0.8808 (mp0) cc_final: 0.8525 (mt-10) REVERT: B 159 TYR cc_start: 0.9100 (t80) cc_final: 0.8522 (t80) REVERT: B 223 SER cc_start: 0.8532 (m) cc_final: 0.8146 (p) outliers start: 12 outliers final: 8 residues processed: 76 average time/residue: 1.2897 time to fit residues: 103.9691 Evaluate side-chains 69 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET 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 38 VAL Chi-restraints excluded: chain B residue 255 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 24 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3257 r_free = 0.3257 target = 0.083268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.068672 restraints weight = 13390.067| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.19 r_work: 0.2853 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7613 Z= 0.151 Angle : 0.541 7.764 10325 Z= 0.298 Chirality : 0.040 0.124 1164 Planarity : 0.003 0.034 1290 Dihedral : 10.275 56.181 1245 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.34 % Allowed : 21.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.28), residues: 918 helix: 0.96 (0.26), residues: 420 sheet: -0.31 (0.41), residues: 159 loop : -1.31 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 294 PHE 0.006 0.001 PHE C 126 TYR 0.010 0.001 TYR C 315 ARG 0.008 0.000 ARG B 27 *********************** 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 73 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8732 (mppt) REVERT: A 43 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8508 (mt-10) REVERT: C 39 LYS cc_start: 0.9221 (mppt) cc_final: 0.8794 (mmtm) REVERT: C 43 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (mt-10) REVERT: B 43 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 159 TYR cc_start: 0.9116 (t80) cc_final: 0.8593 (t80) REVERT: B 223 SER cc_start: 0.8510 (m) cc_final: 0.8132 (p) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.2536 time to fit residues: 93.1678 Evaluate side-chains 66 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 158 MET 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 38 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 15 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3191 r_free = 0.3191 target = 0.079772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065048 restraints weight = 13415.001| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.18 r_work: 0.2767 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7613 Z= 0.230 Angle : 0.590 7.813 10325 Z= 0.324 Chirality : 0.042 0.134 1164 Planarity : 0.003 0.029 1290 Dihedral : 10.655 64.775 1245 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.79 % Favored : 94.99 % Rotamer: Outliers : 1.61 % Allowed : 21.37 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 918 helix: 1.06 (0.26), residues: 414 sheet: -0.45 (0.41), residues: 165 loop : -1.40 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.006 0.001 PHE C 126 TYR 0.017 0.001 TYR A 315 ARG 0.007 0.000 ARG B 27 *********************** 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 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8780 (mmtp) REVERT: A 43 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8499 (mt-10) REVERT: C 39 LYS cc_start: 0.9222 (mppt) cc_final: 0.8903 (mppt) REVERT: C 43 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: B 43 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8506 (mt-10) REVERT: B 184 ASP cc_start: 0.8930 (m-30) cc_final: 0.8621 (m-30) REVERT: B 306 ARG cc_start: 0.8282 (mmp-170) cc_final: 0.8058 (mmp-170) outliers start: 12 outliers final: 10 residues processed: 73 average time/residue: 1.3282 time to fit residues: 103.3319 Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS 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 218 LEU 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 B residue 38 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 125 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 80 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 92 optimal weight: 0.3980 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3159 r_free = 0.3159 target = 0.078279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.063549 restraints weight = 13337.712| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.17 r_work: 0.2729 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7613 Z= 0.279 Angle : 0.617 7.734 10325 Z= 0.339 Chirality : 0.042 0.136 1164 Planarity : 0.004 0.036 1290 Dihedral : 11.013 70.841 1245 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.79 % Favored : 94.88 % Rotamer: Outliers : 1.61 % Allowed : 22.04 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.67 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.28), residues: 918 helix: 1.01 (0.26), residues: 414 sheet: -0.35 (0.42), residues: 165 loop : -1.44 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 294 PHE 0.008 0.001 PHE C 126 TYR 0.018 0.001 TYR A 315 ARG 0.006 0.001 ARG B 27 *********************** 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 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8502 (mt-10) REVERT: A 306 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7852 (mmp-170) REVERT: C 39 LYS cc_start: 0.9244 (mppt) cc_final: 0.8924 (mppt) REVERT: C 43 GLU cc_start: 0.8806 (mp0) cc_final: 0.8529 (mt-10) REVERT: B 43 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8510 (mt-10) REVERT: B 184 ASP cc_start: 0.8957 (m-30) cc_final: 0.8651 (m-30) outliers start: 12 outliers final: 11 residues processed: 69 average time/residue: 1.3777 time to fit residues: 100.3875 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 125 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 78 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3196 r_free = 0.3196 target = 0.080180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.065513 restraints weight = 13292.977| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 2.19 r_work: 0.2776 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7613 Z= 0.197 Angle : 0.579 7.668 10325 Z= 0.318 Chirality : 0.041 0.124 1164 Planarity : 0.003 0.029 1290 Dihedral : 10.798 68.119 1245 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.66 % Rotamer: Outliers : 1.08 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.28), residues: 918 helix: 1.08 (0.26), residues: 414 sheet: -0.40 (0.42), residues: 165 loop : -1.36 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 294 PHE 0.006 0.001 PHE C 126 TYR 0.013 0.001 TYR C 315 ARG 0.006 0.000 ARG B 27 ********************** 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 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8475 (mt-10) REVERT: C 43 GLU cc_start: 0.8808 (mp0) cc_final: 0.8526 (mt-10) REVERT: B 43 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8507 (mt-10) REVERT: B 223 SER cc_start: 0.8681 (m) cc_final: 0.8277 (p) outliers start: 8 outliers final: 9 residues processed: 67 average time/residue: 1.4169 time to fit residues: 100.2702 Evaluate side-chains 68 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 50 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 72 optimal weight: 0.0980 chunk 48 optimal weight: 0.0370 chunk 9 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.2858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3285 r_free = 0.3285 target = 0.084821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.070283 restraints weight = 13240.625| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.22 r_work: 0.2888 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7613 Z= 0.141 Angle : 0.554 7.772 10325 Z= 0.302 Chirality : 0.040 0.135 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.322 58.377 1245 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.08 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.29), residues: 918 helix: 0.97 (0.26), residues: 432 sheet: -0.51 (0.41), residues: 171 loop : -0.98 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 294 PHE 0.007 0.001 PHE A 248 TYR 0.007 0.001 TYR C 159 ARG 0.010 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4768.46 seconds wall clock time: 85 minutes 5.10 seconds (5105.10 seconds total)