Starting phenix.real_space_refine on Tue Feb 13 09:53:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n0k_24107/02_2024/7n0k_24107.pdb" } resolution = 3.5 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= 0.002 sd= 0.073 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3404 2.51 5 N 852 2.21 5 O 868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 22": "OD1" <-> "OD2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B GLU 98": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 22": "OD1" <-> "OD2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5154 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2577 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2577 Classifications: {'peptide': 313} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 306} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 39 Time building chain proxies: 3.12, per 1000 atoms: 0.61 Number of scatterers: 5154 At special positions: 0 Unit cell: (97.85, 91.67, 90.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 868 8.00 N 852 7.00 C 3404 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 877.3 milliseconds 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1188 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 88.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'B' and resid 9 through 68 removed outlier: 4.273A pdb=" N TRP B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B 35 " --> pdb=" O ARG B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 101 removed outlier: 3.907A pdb=" N ALA B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR B 100 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 Processing helix chain 'B' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE B 143 " --> pdb=" O TYR B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 186 removed outlier: 3.698A pdb=" N ILE B 177 " --> pdb=" O CYS B 173 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 209 removed outlier: 4.079A pdb=" N VAL B 194 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 201 " --> pdb=" O HIS B 197 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU B 208 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS B 218 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 250 removed outlier: 3.968A pdb=" N PHE B 226 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 243 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 298 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 305 through 335 removed outlier: 3.857A pdb=" N MET B 309 " --> pdb=" O TRP B 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Proline residue: B 313 - end of helix removed outlier: 3.585A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 68 removed outlier: 4.273A pdb=" N TRP A 16 " --> pdb=" O CYS A 12 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 101 removed outlier: 3.906A pdb=" N ALA A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 122 through 154 removed outlier: 3.832A pdb=" N LYS A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 143 " --> pdb=" O TYR A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 186 removed outlier: 3.699A pdb=" N ILE A 177 " --> pdb=" O CYS A 173 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 209 removed outlier: 4.078A pdb=" N VAL A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR A 198 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.585A pdb=" N LYS A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 250 removed outlier: 3.967A pdb=" N PHE A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 243 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 298 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 305 through 335 removed outlier: 3.858A pdb=" N MET A 309 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Proline residue: A 313 - end of helix removed outlier: 3.584A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 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: 1.23 - 1.34: 1576 1.34 - 1.46: 1379 1.46 - 1.58: 2297 1.58 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 5296 Sorted by residual: bond pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.25e+00 bond pdb=" C TRP A 210 " pdb=" N PRO A 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.61e-01 bond pdb=" C TRP B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.20e-02 6.94e+03 7.52e-01 bond pdb=" N GLY A 213 " pdb=" CA GLY A 213 " ideal model delta sigma weight residual 1.455 1.447 0.008 1.05e-02 9.07e+03 5.51e-01 ... (remaining 5291 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 91 107.15 - 113.86: 2869 113.86 - 120.58: 2417 120.58 - 127.29: 1727 127.29 - 134.01: 60 Bond angle restraints: 7164 Sorted by residual: angle pdb=" CA GLN B 124 " pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " ideal model delta sigma weight residual 114.10 121.77 -7.67 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA GLN A 124 " pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 angle pdb=" CB GLN A 124 " pdb=" CG GLN A 124 " pdb=" CD GLN A 124 " ideal model delta sigma weight residual 112.60 116.00 -3.40 1.70e+00 3.46e-01 3.99e+00 angle pdb=" CB GLN B 124 " pdb=" CG GLN B 124 " pdb=" CD GLN B 124 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.70e+00 3.46e-01 3.93e+00 angle pdb=" CA LEU A 120 " pdb=" CB LEU A 120 " pdb=" CG LEU A 120 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.35e+00 ... (remaining 7159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 2586 17.87 - 35.74: 340 35.74 - 53.62: 92 53.62 - 71.49: 14 71.49 - 89.36: 14 Dihedral angle restraints: 3046 sinusoidal: 1208 harmonic: 1838 Sorted by residual: dihedral pdb=" CA LEU B 120 " pdb=" C LEU B 120 " pdb=" N LEU B 121 " pdb=" CA LEU B 121 " ideal model delta harmonic sigma weight residual -180.00 -163.02 -16.98 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LEU A 120 " pdb=" C LEU A 120 " pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU A 60 " pdb=" CG GLU A 60 " pdb=" CD GLU A 60 " pdb=" OE1 GLU A 60 " ideal model delta sinusoidal sigma weight residual 0.00 -89.36 89.36 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 498 0.025 - 0.050: 203 0.050 - 0.075: 53 0.075 - 0.100: 9 0.100 - 0.125: 9 Chirality restraints: 772 Sorted by residual: chirality pdb=" CA VAL A 112 " pdb=" N VAL A 112 " pdb=" C VAL A 112 " pdb=" CB VAL A 112 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE B 189 " pdb=" N ILE B 189 " pdb=" C ILE B 189 " pdb=" CB ILE B 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 769 not shown) Planarity restraints: 888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 312 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO B 313 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 313 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 313 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 312 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 313 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 313 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 313 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 69 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 70 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.017 5.00e-02 4.00e+02 ... (remaining 885 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1129 2.77 - 3.30: 5182 3.30 - 3.84: 8155 3.84 - 4.37: 9401 4.37 - 4.90: 15378 Nonbonded interactions: 39245 Sorted by model distance: nonbonded pdb=" O LYS A 137 " pdb=" OG1 THR A 141 " model vdw 2.238 2.440 nonbonded pdb=" O LYS B 137 " pdb=" OG1 THR B 141 " model vdw 2.239 2.440 nonbonded pdb=" O GLN A 44 " pdb=" OG1 THR A 48 " model vdw 2.266 2.440 nonbonded pdb=" O GLN B 44 " pdb=" OG1 THR B 48 " model vdw 2.266 2.440 nonbonded pdb=" O GLU A 38 " pdb=" OG1 THR A 41 " model vdw 2.310 2.440 ... (remaining 39240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 3.770 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.510 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.003 0.034 5296 Z= 0.197 Angle : 0.558 7.672 7164 Z= 0.320 Chirality : 0.031 0.125 772 Planarity : 0.003 0.035 888 Dihedral : 18.365 89.361 1858 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 7.46 % Allowed : 17.16 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.20 (0.29), residues: 614 helix: -1.29 (0.18), residues: 526 sheet: None (None), residues: 0 loop : -1.07 (0.76), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.003 0.001 HIS A 196 PHE 0.007 0.001 PHE B 127 TYR 0.007 0.001 TYR A 172 ARG 0.005 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7238 (t80) cc_final: 0.6972 (t80) REVERT: A 127 PHE cc_start: 0.7398 (t80) cc_final: 0.7135 (t80) REVERT: A 183 ILE cc_start: 0.7261 (mm) cc_final: 0.6926 (mt) REVERT: A 228 MET cc_start: 0.7126 (mtm) cc_final: 0.6891 (ttm) outliers start: 40 outliers final: 22 residues processed: 130 average time/residue: 0.1612 time to fit residues: 27.0133 Evaluate side-chains 90 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 68 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 0.0770 chunk 48 optimal weight: 0.0170 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS B 197 HIS B 234 GLN B 241 GLN B 286 GLN A 54 GLN A 184 ASN A 196 HIS A 197 HIS A 241 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5296 Z= 0.165 Angle : 0.549 8.751 7164 Z= 0.281 Chirality : 0.033 0.121 772 Planarity : 0.005 0.056 888 Dihedral : 8.208 86.917 718 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.36 % Allowed : 23.13 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.32 (0.31), residues: 614 helix: 1.32 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -2.37 (0.62), residues: 72 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 192 HIS 0.004 0.001 HIS A 30 PHE 0.014 0.001 PHE B 195 TYR 0.014 0.001 TYR B 240 ARG 0.003 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 81 time to evaluate : 0.628 Fit side-chains REVERT: B 234 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7369 (mm-40) REVERT: B 291 LEU cc_start: 0.8991 (mm) cc_final: 0.8525 (tt) REVERT: A 87 MET cc_start: 0.7340 (tpp) cc_final: 0.6814 (tpt) outliers start: 18 outliers final: 10 residues processed: 98 average time/residue: 0.1612 time to fit residues: 20.8498 Evaluate side-chains 79 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN A 30 HIS A 54 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5296 Z= 0.176 Angle : 0.506 5.756 7164 Z= 0.257 Chirality : 0.034 0.137 772 Planarity : 0.004 0.046 888 Dihedral : 7.311 89.056 703 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.17 % Allowed : 26.87 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.38 (0.32), residues: 614 helix: 2.02 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -1.84 (0.64), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.007 0.001 PHE A 195 TYR 0.015 0.001 TYR B 240 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 0.553 Fit side-chains REVERT: B 127 PHE cc_start: 0.7408 (t80) cc_final: 0.6447 (m-10) REVERT: B 179 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6583 (mt-10) REVERT: B 207 MET cc_start: 0.7810 (tpp) cc_final: 0.7363 (tpp) REVERT: B 291 LEU cc_start: 0.8913 (mm) cc_final: 0.8682 (mp) REVERT: A 87 MET cc_start: 0.7471 (tpp) cc_final: 0.6933 (tpt) REVERT: A 88 LYS cc_start: 0.8385 (mtmt) cc_final: 0.8132 (mtmt) REVERT: A 127 PHE cc_start: 0.7402 (t80) cc_final: 0.6564 (m-10) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.1334 time to fit residues: 16.8311 Evaluate side-chains 85 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5296 Z= 0.173 Angle : 0.512 7.955 7164 Z= 0.254 Chirality : 0.034 0.140 772 Planarity : 0.003 0.033 888 Dihedral : 6.941 87.495 701 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.66 % Allowed : 27.24 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.85 (0.32), residues: 614 helix: 2.37 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.88 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.006 0.001 PHE A 235 TYR 0.015 0.001 TYR B 240 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: B 179 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6609 (mt-10) REVERT: B 208 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (tp) REVERT: B 291 LEU cc_start: 0.8887 (mm) cc_final: 0.8643 (mp) REVERT: A 127 PHE cc_start: 0.7312 (t80) cc_final: 0.6552 (m-10) REVERT: A 208 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7838 (tp) outliers start: 25 outliers final: 16 residues processed: 89 average time/residue: 0.1165 time to fit residues: 14.8499 Evaluate side-chains 80 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5296 Z= 0.239 Angle : 0.564 8.548 7164 Z= 0.272 Chirality : 0.036 0.132 772 Planarity : 0.003 0.029 888 Dihedral : 6.811 88.333 699 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.72 % Allowed : 27.05 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.92 (0.33), residues: 614 helix: 2.42 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.94 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 210 HIS 0.001 0.001 HIS A 196 PHE 0.009 0.001 PHE A 235 TYR 0.015 0.002 TYR B 240 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 73 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7250 (t80) cc_final: 0.6371 (m-10) REVERT: B 208 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7878 (tp) REVERT: B 240 TYR cc_start: 0.7363 (t80) cc_final: 0.7149 (t80) REVERT: B 291 LEU cc_start: 0.8919 (mm) cc_final: 0.8677 (mp) REVERT: A 127 PHE cc_start: 0.7289 (t80) cc_final: 0.6435 (m-10) REVERT: A 208 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7885 (tp) REVERT: A 230 GLN cc_start: 0.7420 (tt0) cc_final: 0.7212 (tt0) outliers start: 36 outliers final: 24 residues processed: 103 average time/residue: 0.1172 time to fit residues: 17.2482 Evaluate side-chains 97 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5296 Z= 0.207 Angle : 0.551 8.744 7164 Z= 0.264 Chirality : 0.035 0.129 772 Planarity : 0.003 0.029 888 Dihedral : 6.614 88.299 699 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.97 % Allowed : 30.41 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.97 (0.33), residues: 614 helix: 2.46 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.87 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.001 0.000 HIS A 196 PHE 0.008 0.001 PHE A 235 TYR 0.014 0.002 TYR B 238 ARG 0.007 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 127 PHE cc_start: 0.7185 (t80) cc_final: 0.6328 (m-10) REVERT: B 208 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7860 (tp) REVERT: B 291 LEU cc_start: 0.8991 (mm) cc_final: 0.8767 (mp) REVERT: A 127 PHE cc_start: 0.7207 (t80) cc_final: 0.6328 (m-10) REVERT: A 230 GLN cc_start: 0.7397 (tt0) cc_final: 0.7191 (tt0) outliers start: 32 outliers final: 23 residues processed: 101 average time/residue: 0.1188 time to fit residues: 17.1779 Evaluate side-chains 92 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 304 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 37 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN A 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5296 Z= 0.183 Angle : 0.543 9.027 7164 Z= 0.260 Chirality : 0.034 0.128 772 Planarity : 0.003 0.029 888 Dihedral : 6.308 86.915 697 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.41 % Allowed : 31.72 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.14 (0.33), residues: 614 helix: 2.58 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.97 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 210 HIS 0.001 0.000 HIS B 196 PHE 0.012 0.001 PHE A 318 TYR 0.022 0.002 TYR B 240 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 179 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6782 (mt-10) REVERT: B 291 LEU cc_start: 0.8977 (mm) cc_final: 0.8752 (mp) REVERT: B 304 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5981 (mm-30) REVERT: A 127 PHE cc_start: 0.7134 (t80) cc_final: 0.6340 (m-10) REVERT: A 304 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5943 (mm-30) outliers start: 29 outliers final: 22 residues processed: 91 average time/residue: 0.1192 time to fit residues: 15.5706 Evaluate side-chains 90 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 0.6980 chunk 37 optimal weight: 0.0470 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN B 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5296 Z= 0.179 Angle : 0.543 9.170 7164 Z= 0.261 Chirality : 0.034 0.133 772 Planarity : 0.003 0.029 888 Dihedral : 5.981 87.375 695 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 6.72 % Allowed : 31.53 % Favored : 61.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.26 (0.33), residues: 614 helix: 2.66 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.94 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS B 196 PHE 0.010 0.001 PHE A 318 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 69 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8972 (mm) cc_final: 0.8745 (mp) REVERT: B 304 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.6042 (mm-30) REVERT: A 127 PHE cc_start: 0.7115 (t80) cc_final: 0.6348 (m-10) outliers start: 36 outliers final: 27 residues processed: 98 average time/residue: 0.1255 time to fit residues: 17.2619 Evaluate side-chains 99 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 71 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.0980 chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5296 Z= 0.174 Angle : 0.561 10.049 7164 Z= 0.265 Chirality : 0.034 0.130 772 Planarity : 0.003 0.030 888 Dihedral : 5.555 87.863 692 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.22 % Allowed : 32.84 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.42 (0.33), residues: 614 helix: 2.76 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.83 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 210 HIS 0.001 0.000 HIS A 30 PHE 0.008 0.001 PHE A 318 TYR 0.023 0.001 TYR B 240 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 291 LEU cc_start: 0.8985 (mm) cc_final: 0.8755 (mp) REVERT: A 84 GLU cc_start: 0.6586 (tm-30) cc_final: 0.6285 (tm-30) REVERT: A 240 TYR cc_start: 0.7094 (t80) cc_final: 0.6663 (t80) outliers start: 28 outliers final: 24 residues processed: 93 average time/residue: 0.1289 time to fit residues: 16.8810 Evaluate side-chains 93 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 69 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5296 Z= 0.194 Angle : 0.579 10.333 7164 Z= 0.274 Chirality : 0.034 0.126 772 Planarity : 0.003 0.030 888 Dihedral : 3.838 17.126 686 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.29 % Allowed : 34.33 % Favored : 61.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.40 (0.33), residues: 614 helix: 2.76 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.93 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 210 HIS 0.001 0.000 HIS A 196 PHE 0.010 0.001 PHE A 94 TYR 0.015 0.001 TYR A 240 ARG 0.005 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1228 Ramachandran restraints generated. 614 Oldfield, 0 Emsley, 614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: B 88 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7864 (mtmt) REVERT: B 240 TYR cc_start: 0.7236 (t80) cc_final: 0.6826 (t80) REVERT: B 291 LEU cc_start: 0.8980 (mm) cc_final: 0.8747 (mp) REVERT: A 84 GLU cc_start: 0.6546 (tm-30) cc_final: 0.6230 (tm-30) outliers start: 23 outliers final: 22 residues processed: 88 average time/residue: 0.1417 time to fit residues: 17.3104 Evaluate side-chains 92 residues out of total 572 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 HIS Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain A residue 18 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 0.0030 chunk 50 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.206243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164477 restraints weight = 5768.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.168525 restraints weight = 3362.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.170962 restraints weight = 2434.317| |-----------------------------------------------------------------------------| r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5296 Z= 0.181 Angle : 0.581 10.456 7164 Z= 0.275 Chirality : 0.034 0.129 772 Planarity : 0.003 0.048 888 Dihedral : 3.821 17.148 686 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.48 % Allowed : 33.58 % Favored : 61.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3.48 (0.33), residues: 614 helix: 2.81 (0.21), residues: 538 sheet: None (None), residues: 0 loop : -1.83 (0.69), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 210 HIS 0.001 0.000 HIS A 30 PHE 0.010 0.001 PHE A 94 TYR 0.022 0.001 TYR A 240 ARG 0.009 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1180.11 seconds wall clock time: 21 minutes 59.33 seconds (1319.33 seconds total)