Starting phenix.real_space_refine on Sat Dec 28 05:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ejc_31158/12_2024/7ejc_31158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ejc_31158/12_2024/7ejc_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_31158/12_2024/7ejc_31158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ejc_31158/12_2024/7ejc_31158.map" model { file = "/net/cci-nas-00/data/ceres_data/7ejc_31158/12_2024/7ejc_31158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ejc_31158/12_2024/7ejc_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-5532/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: 5.68, per 1000 atoms: 0.76 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: 2.10 Conformation dependent library (CDL) restraints added in 975.0 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: 0.82 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: 2.09 Time building geometry restraints manager: 2.30 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: 4.380 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.920 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.060 ------------------------------------------------------------------------------- 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 : 0.881 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: 1.5490 time to fit residues: 207.3530 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 : 0.846 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASN cc_start: 0.8308 (t0) cc_final: 0.8105 (t0) REVERT: A 322 GLU cc_start: 0.8325 (tt0) cc_final: 0.7955 (tp30) REVERT: A 326 MET cc_start: 0.8668 (ttp) cc_final: 0.8418 (ttp) REVERT: C 322 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: C 326 MET cc_start: 0.8378 (ttm) cc_final: 0.7967 (ttp) REVERT: B 43 GLU cc_start: 0.8562 (mp0) cc_final: 0.8271 (mt-10) REVERT: B 159 TYR cc_start: 0.8565 (t80) cc_final: 0.7749 (t80) outliers start: 21 outliers final: 10 residues processed: 96 average time/residue: 1.4351 time to fit residues: 145.8327 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 C residue 322 GLU 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 47 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7613 Z= 0.206 Angle : 0.595 7.437 10325 Z= 0.327 Chirality : 0.041 0.131 1164 Planarity : 0.004 0.039 1290 Dihedral : 10.926 57.163 1248 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.68 % Favored : 95.10 % Rotamer: Outliers : 2.82 % Allowed : 17.34 % Favored : 79.84 % 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: -1.18 (0.27), residues: 918 helix: 0.40 (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 0.008 0.001 PHE B 126 TYR 0.016 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 93 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (mmtp) REVERT: A 43 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: A 184 ASP cc_start: 0.8716 (m-30) cc_final: 0.8496 (p0) REVERT: A 322 GLU cc_start: 0.8317 (tt0) cc_final: 0.7939 (tp30) REVERT: A 326 MET cc_start: 0.8592 (ttp) cc_final: 0.8323 (ttp) REVERT: C 39 LYS cc_start: 0.9024 (mppt) cc_final: 0.8662 (mmtm) REVERT: C 184 ASP cc_start: 0.8955 (m-30) cc_final: 0.8742 (m-30) REVERT: C 322 GLU cc_start: 0.8322 (tt0) cc_final: 0.8009 (tp30) REVERT: B 43 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: B 159 TYR cc_start: 0.8694 (t80) cc_final: 0.7725 (t80) REVERT: B 184 ASP cc_start: 0.8930 (m-30) cc_final: 0.8682 (m-30) REVERT: B 189 VAL cc_start: 0.7007 (OUTLIER) cc_final: 0.6779 (m) outliers start: 21 outliers final: 10 residues processed: 86 average time/residue: 1.3483 time to fit residues: 122.7811 Evaluate side-chains 80 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 38 VAL 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 189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2911 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= 0.169 Angle : 0.563 7.525 10325 Z= 0.311 Chirality : 0.040 0.158 1164 Planarity : 0.003 0.034 1290 Dihedral : 10.635 57.260 1245 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.42 % Allowed : 18.15 % 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: -0.71 (0.27), residues: 918 helix: 0.76 (0.27), residues: 411 sheet: -0.62 (0.40), residues: 162 loop : -1.89 (0.29), residues: 345 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 0.012 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 89 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8578 (mp0) cc_final: 0.8220 (mt-10) REVERT: A 184 ASP cc_start: 0.8716 (m-30) cc_final: 0.8491 (p0) REVERT: A 322 GLU cc_start: 0.8331 (tt0) cc_final: 0.7984 (tp30) REVERT: A 326 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8268 (ttp) REVERT: C 39 LYS cc_start: 0.9021 (mppt) cc_final: 0.8649 (mmtm) REVERT: C 322 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: B 43 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: B 189 VAL cc_start: 0.6683 (OUTLIER) cc_final: 0.6467 (m) REVERT: B 223 SER cc_start: 0.8226 (m) cc_final: 0.7653 (p) outliers start: 18 outliers final: 8 residues processed: 82 average time/residue: 1.2415 time to fit residues: 107.9727 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 326 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 C residue 322 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 43 GLU 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 51 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 0.0010 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.0020 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 0.0670 chunk 81 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5334 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3259 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= 0.141 Angle : 0.529 7.632 10325 Z= 0.293 Chirality : 0.040 0.127 1164 Planarity : 0.003 0.025 1290 Dihedral : 10.332 54.506 1245 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.48 % Allowed : 19.76 % Favored : 78.76 % 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: -0.48 (0.28), residues: 918 helix: 0.92 (0.26), residues: 420 sheet: -0.63 (0.41), residues: 165 loop : -1.73 (0.31), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 294 PHE 0.007 0.001 PHE C 126 TYR 0.009 0.001 TYR C 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 93 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8604 (mp0) cc_final: 0.8210 (mt-10) REVERT: A 184 ASP cc_start: 0.8669 (m-30) cc_final: 0.8432 (p0) REVERT: A 322 GLU cc_start: 0.8338 (tt0) cc_final: 0.7976 (tp30) REVERT: A 326 MET cc_start: 0.8531 (ttp) cc_final: 0.8262 (ttp) REVERT: C 39 LYS cc_start: 0.9043 (mppt) cc_final: 0.8646 (mmtm) REVERT: C 43 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8219 (mt-10) REVERT: C 184 ASP cc_start: 0.8869 (m-30) cc_final: 0.8620 (p0) REVERT: B 43 GLU cc_start: 0.8562 (mp0) cc_final: 0.8226 (mt-10) REVERT: B 184 ASP cc_start: 0.8866 (m-30) cc_final: 0.8531 (p0) REVERT: B 223 SER cc_start: 0.8111 (m) cc_final: 0.7541 (p) outliers start: 11 outliers final: 6 residues processed: 90 average time/residue: 1.2947 time to fit residues: 123.2732 Evaluate side-chains 70 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 81 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7613 Z= 0.175 Angle : 0.556 7.713 10325 Z= 0.307 Chirality : 0.041 0.130 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.382 57.662 1245 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.34 % Allowed : 20.83 % Favored : 77.82 % 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: -0.30 (0.28), residues: 918 helix: 0.99 (0.27), residues: 417 sheet: -0.46 (0.41), residues: 165 loop : -1.54 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 294 PHE 0.006 0.001 PHE C 327 TYR 0.013 0.001 TYR A 315 ARG 0.006 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 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8564 (mppt) REVERT: A 43 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8184 (mt-10) REVERT: A 184 ASP cc_start: 0.8719 (m-30) cc_final: 0.8477 (p0) REVERT: A 324 GLU cc_start: 0.8644 (pt0) cc_final: 0.8185 (mt-10) REVERT: A 326 MET cc_start: 0.8502 (ttp) cc_final: 0.8187 (ttp) REVERT: C 39 LYS cc_start: 0.9060 (mppt) cc_final: 0.8637 (mmtm) REVERT: C 43 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: C 184 ASP cc_start: 0.8886 (m-30) cc_final: 0.8614 (m-30) REVERT: B 43 GLU cc_start: 0.8552 (mp0) cc_final: 0.8192 (mt-10) REVERT: B 159 TYR cc_start: 0.8760 (t80) cc_final: 0.7761 (t80) REVERT: B 213 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7702 (tm-30) outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 1.3067 time to fit residues: 99.8280 Evaluate side-chains 71 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 50 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.003 0.035 7613 Z= 0.171 Angle : 0.550 7.746 10325 Z= 0.303 Chirality : 0.040 0.125 1164 Planarity : 0.003 0.021 1290 Dihedral : 10.399 59.782 1245 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.61 % Allowed : 21.10 % 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: -0.13 (0.28), residues: 918 helix: 1.08 (0.26), residues: 417 sheet: -0.45 (0.41), residues: 165 loop : -1.33 (0.32), residues: 336 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 0.012 0.001 TYR A 315 ARG 0.007 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 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8576 (mppt) REVERT: A 43 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 184 ASP cc_start: 0.8722 (m-30) cc_final: 0.8472 (p0) REVERT: A 324 GLU cc_start: 0.8625 (pt0) cc_final: 0.8190 (mt-10) REVERT: A 326 MET cc_start: 0.8496 (ttp) cc_final: 0.8193 (ttp) REVERT: C 39 LYS cc_start: 0.9063 (mppt) cc_final: 0.8647 (mmtm) REVERT: C 43 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: C 184 ASP cc_start: 0.8869 (m-30) cc_final: 0.8590 (m-30) REVERT: B 43 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8169 (mt-10) REVERT: B 159 TYR cc_start: 0.8823 (t80) cc_final: 0.7769 (t80) REVERT: B 189 VAL cc_start: 0.6497 (OUTLIER) cc_final: 0.6239 (m) REVERT: B 223 SER cc_start: 0.8243 (m) cc_final: 0.7682 (p) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 1.3308 time to fit residues: 105.6703 Evaluate side-chains 72 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 38 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3420 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= 0.167 Angle : 0.554 7.761 10325 Z= 0.305 Chirality : 0.040 0.125 1164 Planarity : 0.003 0.022 1290 Dihedral : 10.372 60.331 1245 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.02 % Allowed : 21.37 % Favored : 76.61 % 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: -0.04 (0.28), residues: 918 helix: 1.15 (0.26), residues: 417 sheet: -0.45 (0.41), residues: 165 loop : -1.25 (0.33), residues: 336 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 0.012 0.001 TYR A 315 ARG 0.006 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 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8618 (mmtp) REVERT: A 43 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8217 (mt-10) REVERT: A 184 ASP cc_start: 0.8730 (m-30) cc_final: 0.8481 (p0) REVERT: A 324 GLU cc_start: 0.8601 (pt0) cc_final: 0.8189 (mt-10) REVERT: A 326 MET cc_start: 0.8496 (ttp) cc_final: 0.8192 (ttp) REVERT: C 43 GLU cc_start: 0.8566 (mp0) cc_final: 0.8205 (mt-10) REVERT: C 184 ASP cc_start: 0.8857 (m-30) cc_final: 0.8570 (m-30) REVERT: B 43 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8193 (mt-10) REVERT: B 159 TYR cc_start: 0.8855 (t80) cc_final: 0.7801 (t80) REVERT: B 189 VAL cc_start: 0.6501 (OUTLIER) cc_final: 0.6234 (m) REVERT: B 213 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 223 SER cc_start: 0.8260 (m) cc_final: 0.7697 (p) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 1.2594 time to fit residues: 100.4901 Evaluate side-chains 74 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 C residue 218 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7613 Z= 0.166 Angle : 0.549 7.822 10325 Z= 0.302 Chirality : 0.040 0.127 1164 Planarity : 0.003 0.021 1290 Dihedral : 10.361 60.987 1245 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.88 % Allowed : 21.77 % 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: 0.04 (0.28), residues: 918 helix: 1.20 (0.26), residues: 417 sheet: -0.46 (0.41), residues: 165 loop : -1.17 (0.33), residues: 336 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 0.012 0.001 TYR A 315 ARG 0.005 0.000 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 80 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8650 (mppt) REVERT: A 43 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8215 (mt-10) REVERT: A 213 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 324 GLU cc_start: 0.8589 (pt0) cc_final: 0.8201 (mt-10) REVERT: A 326 MET cc_start: 0.8492 (ttp) cc_final: 0.8195 (ttp) REVERT: C 43 GLU cc_start: 0.8560 (mp0) cc_final: 0.8201 (mt-10) REVERT: C 184 ASP cc_start: 0.8854 (m-30) cc_final: 0.8560 (m-30) REVERT: B 43 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8187 (mt-10) REVERT: B 189 VAL cc_start: 0.6459 (OUTLIER) cc_final: 0.6178 (m) REVERT: B 213 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7614 (tm-30) REVERT: B 223 SER cc_start: 0.8247 (m) cc_final: 0.7688 (p) outliers start: 14 outliers final: 10 residues processed: 78 average time/residue: 1.2724 time to fit residues: 105.3733 Evaluate side-chains 75 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3424 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= 0.205 Angle : 0.583 7.865 10325 Z= 0.319 Chirality : 0.041 0.129 1164 Planarity : 0.003 0.027 1290 Dihedral : 10.537 64.890 1245 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.75 % Allowed : 21.91 % 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: 0.01 (0.28), residues: 918 helix: 1.19 (0.26), residues: 417 sheet: -0.41 (0.41), residues: 165 loop : -1.23 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 294 PHE 0.006 0.001 PHE C 126 TYR 0.015 0.001 TYR A 315 ARG 0.005 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 78 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8652 (mppt) REVERT: A 43 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8206 (mt-10) REVERT: A 324 GLU cc_start: 0.8606 (pt0) cc_final: 0.8175 (mt-10) REVERT: A 326 MET cc_start: 0.8482 (ttp) cc_final: 0.8184 (ttp) REVERT: C 39 LYS cc_start: 0.9077 (mppt) cc_final: 0.8768 (mppt) REVERT: C 43 GLU cc_start: 0.8553 (mp0) cc_final: 0.8181 (mt-10) REVERT: C 184 ASP cc_start: 0.8866 (m-30) cc_final: 0.8585 (m-30) REVERT: B 43 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 184 ASP cc_start: 0.8845 (m-30) cc_final: 0.8505 (m-30) REVERT: B 213 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7701 (tm-30) outliers start: 13 outliers final: 12 residues processed: 76 average time/residue: 1.3142 time to fit residues: 105.7829 Evaluate side-chains 76 residues out of total 744 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.886 ------------------------------------------------------------------------------- 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 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 97 SER 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 68 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.3202 r_free = 0.3202 target = 0.080428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.065823 restraints weight = 13163.628| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.20 r_work: 0.2788 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9007 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7613 Z= 0.199 Angle : 0.586 8.231 10325 Z= 0.319 Chirality : 0.041 0.125 1164 Planarity : 0.003 0.026 1290 Dihedral : 10.597 66.505 1245 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.61 % Allowed : 22.45 % 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: 0.03 (0.28), residues: 918 helix: 1.19 (0.26), residues: 417 sheet: -0.40 (0.41), residues: 165 loop : -1.19 (0.33), residues: 336 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 0.014 0.001 TYR A 315 ARG 0.009 0.000 ARG C 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2715.29 seconds wall clock time: 49 minutes 36.85 seconds (2976.85 seconds total)