Starting phenix.real_space_refine on Mon Jul 22 05:58:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/07_2024/8tzk_41761_neut.cif" } resolution = 3.55 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= 0.000 sd= 0.017 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 P 4 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 5491 2.51 5 N 1550 2.21 5 O 1535 1.98 5 H 8468 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17077 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3494 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4369 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved non-hydrogen bonds: 173 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 10, 'ASP:plan': 9, 'ARG:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4359 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 93 Chain: "E" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1305 Classifications: {'peptide': 101} Link IDs: {'TRANS': 100} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.12, per 1000 atoms: 0.53 Number of scatterers: 17077 At special positions: 0 Unit cell: (105.84, 83.16, 149.04, 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) S 27 16.00 P 4 15.00 Mg 2 11.99 O 1535 8.00 N 1550 7.00 C 5491 6.00 H 8468 1.00 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: 12.53 Conformation dependent library (CDL) restraints added in 1.9 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 62.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.651A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 89 removed outlier: 3.784A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Proline residue: A 112 - end of helix removed outlier: 3.739A pdb=" N GLU A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 178 through 196 removed outlier: 3.709A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 212 removed outlier: 3.770A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.648A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.766A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 116 Proline residue: B 112 - end of helix removed outlier: 3.759A pdb=" N GLU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 134 Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 178 through 196 removed outlier: 3.671A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 removed outlier: 3.766A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 removed outlier: 3.511A pdb=" N ILE C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 86 removed outlier: 3.604A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Proline residue: C 68 - end of helix removed outlier: 4.217A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 removed outlier: 3.571A pdb=" N ILE C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 136 Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 193 through 229 removed outlier: 3.812A pdb=" N HIS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N THR C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 240 Processing helix chain 'C' and resid 242 through 287 Proline residue: C 249 - end of helix removed outlier: 4.651A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 326 removed outlier: 3.909A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.529A pdb=" N HIS D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 85 Proline residue: D 68 - end of helix Processing helix chain 'D' and resid 100 through 114 Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.046A pdb=" N TYR D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'D' and resid 162 through 176 Processing helix chain 'D' and resid 188 through 229 removed outlier: 3.678A pdb=" N LEU D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 242 through 286 removed outlier: 3.570A pdb=" N ILE D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) Proline residue: D 249 - end of helix removed outlier: 3.727A pdb=" N LEU D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 326 removed outlier: 3.632A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 129 removed outlier: 3.632A pdb=" N ARG E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 191 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.945A pdb=" N ILE A 11 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 67 " --> pdb=" O GLN A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18 removed outlier: 3.605A pdb=" N VAL A 16 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LYS A 18 " --> pdb=" O GLN A 28 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN A 28 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40 removed outlier: 5.752A pdb=" N ALA A 40 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 170 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N GLY A 91 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N ASP A 171 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A 93 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.570A pdb=" N GLY A 43 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.920A pdb=" N ILE B 11 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 67 " --> pdb=" O GLN B 14 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.622A pdb=" N VAL B 16 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LYS B 18 " --> pdb=" O GLN B 28 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N GLN B 28 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40 removed outlier: 5.745A pdb=" N ALA B 40 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 170 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLY B 91 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44 removed outlier: 6.571A pdb=" N GLY B 43 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.633A pdb=" N VAL C 153 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 123 removed outlier: 3.978A pdb=" N LYS D 119 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 153 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP D 181 " --> pdb=" O TYR D 94 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1662 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: 6.00 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8462 1.03 - 1.23: 6 1.23 - 1.42: 3534 1.42 - 1.61: 5162 1.61 - 1.81: 54 Bond restraints: 17218 Sorted by residual: bond pdb=" C6 ADP A 302 " pdb=" N6 ADP A 302 " ideal model delta sigma weight residual 1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C6 ADP B 302 " pdb=" N6 ADP B 302 " ideal model delta sigma weight residual 1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C4 ADP A 302 " pdb=" C5 ADP A 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C4 ADP B 302 " pdb=" C5 ADP B 302 " ideal model delta sigma weight residual 1.490 1.397 0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sigma weight residual 1.610 1.684 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 17213 not shown) Histogram of bond angle deviations from ideal: 100.58 - 107.34: 1792 107.34 - 114.11: 19164 114.11 - 120.87: 6409 120.87 - 127.63: 3676 127.63 - 134.39: 75 Bond angle restraints: 31116 Sorted by residual: angle pdb=" O2B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.35 10.55 3.00e+00 1.11e-01 1.24e+01 angle pdb=" O2B ADP A 302 " pdb=" PB ADP A 302 " pdb=" O3B ADP A 302 " ideal model delta sigma weight residual 119.90 109.45 10.45 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N ILE D 239 " pdb=" CA ILE D 239 " pdb=" C ILE D 239 " ideal model delta sigma weight residual 110.21 106.30 3.91 1.13e+00 7.83e-01 1.20e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O3B ADP B 302 " ideal model delta sigma weight residual 119.90 109.67 10.23 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O1B ADP B 302 " pdb=" PB ADP B 302 " pdb=" O2B ADP B 302 " ideal model delta sigma weight residual 119.90 109.72 10.18 3.00e+00 1.11e-01 1.15e+01 ... (remaining 31111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 7770 24.87 - 49.73: 219 49.73 - 74.60: 65 74.60 - 99.46: 1 99.46 - 124.33: 6 Dihedral angle restraints: 8061 sinusoidal: 4289 harmonic: 3772 Sorted by residual: dihedral pdb=" O2A ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PA ADP B 302 " pdb=" PB ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 64.33 -124.33 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" O1B ADP A 302 " pdb=" O3A ADP A 302 " pdb=" PB ADP A 302 " pdb=" PA ADP A 302 " ideal model delta sinusoidal sigma weight residual -60.00 61.90 -121.90 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" O1B ADP B 302 " pdb=" O3A ADP B 302 " pdb=" PB ADP B 302 " pdb=" PA ADP B 302 " ideal model delta sinusoidal sigma weight residual -60.00 59.60 -119.60 1 2.00e+01 2.50e-03 3.59e+01 ... (remaining 8058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1173 0.042 - 0.084: 179 0.084 - 0.126: 61 0.126 - 0.168: 5 0.168 - 0.211: 6 Chirality restraints: 1424 Sorted by residual: chirality pdb=" C2' ADP A 302 " pdb=" C1' ADP A 302 " pdb=" C3' ADP A 302 " pdb=" O2' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C3' ADP A 302 " pdb=" C2' ADP A 302 " pdb=" C4' ADP A 302 " pdb=" O3' ADP A 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C3' ADP B 302 " pdb=" C2' ADP B 302 " pdb=" C4' ADP B 302 " pdb=" O3' ADP B 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 1421 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 87 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01 pdb=" N PRO C 88 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 212 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.54e-01 pdb=" N PRO B 213 " -0.035 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " 0.011 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 101 " 0.012 5.00e-02 4.00e+02 1.84e-02 5.40e-01 pdb=" N PRO C 102 " -0.032 5.00e-02 4.00e+02 pdb=" CA PRO C 102 " 0.009 5.00e-02 4.00e+02 pdb=" CD PRO C 102 " 0.010 5.00e-02 4.00e+02 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 379 2.13 - 2.75: 31413 2.75 - 3.36: 46217 3.36 - 3.98: 55796 3.98 - 4.60: 90294 Nonbonded interactions: 224099 Sorted by model distance: nonbonded pdb=" O GLU B 116 " pdb=" HG SER B 117 " model vdw 1.511 1.850 nonbonded pdb=" O LEU E 122 " pdb=" HG1 THR E 125 " model vdw 1.588 1.850 nonbonded pdb=" O GLU A 116 " pdb=" HG SER A 117 " model vdw 1.623 1.850 nonbonded pdb=" HD1 HIS D 36 " pdb=" OH TYR D 252 " model vdw 1.643 1.850 nonbonded pdb="HE21 GLN A 25 " pdb=" OE1 GLN A 28 " model vdw 1.668 1.850 ... (remaining 224094 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' } ncs_group { reference = (chain 'C' and (resid 27 through 83 or (resid 84 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 85 through 91 or (resid \ 92 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 93 through 99 or (resid 100 and (name N or name CA or name C or name O \ or name CB or name HA )) or resid 101 or (resid 102 and (name N or name CA or n \ ame C or name O or name CB or name HA )) or (resid 103 through 117 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 118 th \ rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 122 through 123 or (resid 124 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 125 through \ 152 or (resid 153 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 154 or (resid 155 through 157 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or (resid 158 and (name N o \ r name CA or name C or name O or name CB or name HA )) or resid 159 through 230 \ or (resid 231 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 232 through 241 or (resid 242 through 243 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 244 throug \ h 291 or (resid 292 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 293 or (resid 294 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 295 through 330)) selection = (chain 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 29 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \ or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD \ 2 or name HE1 or name HE2)) or resid 37 through 82 or (resid 83 through 84 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 85 through 89 or (resid 90 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 91 through 94 or (resid 95 through 96 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 97 through 110 or (resid 111 through 117 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 118 through 148 or (resid 149 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 150 through 162 or (resid 163 through 169 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 170 through 172 or (resid \ 173 through 174 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 175 through 178 or (resid 179 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 180 or (resid 181 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 182 through 183 or (resid 184 through 187 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 188 through 191 or (resid \ 192 through 193 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 194 through 195 or (resid 196 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 197 through 287 or \ (resid 288 and (name N or name CA or name C or name O or name CB or name H or na \ me HA )) or resid 289 through 330)) } 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: 5.700 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: 0.260 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 54.780 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.004 0.095 8750 Z= 0.248 Angle : 0.527 10.553 11890 Z= 0.246 Chirality : 0.037 0.211 1424 Planarity : 0.002 0.021 1509 Dihedral : 11.132 124.329 3110 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 3.24 (0.26), residues: 1139 helix: 3.71 (0.19), residues: 672 sheet: 0.47 (0.56), residues: 103 loop : -0.50 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.002 0.001 HIS B 97 PHE 0.006 0.001 PHE C 257 TYR 0.008 0.001 TYR D 252 ARG 0.003 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 195 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8660 (mmm) cc_final: 0.8317 (mmt) REVERT: C 41 LYS cc_start: 0.8721 (tttt) cc_final: 0.8507 (ttmm) REVERT: C 63 MET cc_start: 0.8253 (mtm) cc_final: 0.7980 (mtt) REVERT: D 223 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7216 (ttp-170) REVERT: E 123 LEU cc_start: 0.9022 (tt) cc_final: 0.8536 (mt) REVERT: E 141 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7580 (tpm170) REVERT: E 170 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8416 (tm-30) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.6357 time to fit residues: 156.1101 Evaluate side-chains 114 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 80 ASN E 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8750 Z= 0.217 Angle : 0.554 6.825 11890 Z= 0.277 Chirality : 0.037 0.167 1424 Planarity : 0.003 0.023 1509 Dihedral : 8.037 136.508 1262 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.33 % Allowed : 8.19 % Favored : 90.48 % 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: 2.95 (0.25), residues: 1139 helix: 3.47 (0.19), residues: 684 sheet: 0.13 (0.54), residues: 100 loop : -0.69 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 256 HIS 0.003 0.001 HIS A 33 PHE 0.017 0.001 PHE C 215 TYR 0.010 0.001 TYR D 250 ARG 0.003 0.000 ARG E 159 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 123 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 101 MET cc_start: 0.8660 (mmm) cc_final: 0.8373 (mmt) REVERT: C 41 LYS cc_start: 0.8711 (tttt) cc_final: 0.8509 (ttmm) REVERT: D 223 ARG cc_start: 0.7477 (ttm-80) cc_final: 0.7257 (ttp-170) REVERT: D 306 MET cc_start: 0.6700 (tmm) cc_final: 0.6460 (tmm) REVERT: E 123 LEU cc_start: 0.9035 (tt) cc_final: 0.8527 (mt) REVERT: E 141 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7609 (tpm170) REVERT: E 170 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8353 (tm-30) outliers start: 11 outliers final: 9 residues processed: 132 average time/residue: 0.5496 time to fit residues: 94.9933 Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8750 Z= 0.273 Angle : 0.540 5.844 11890 Z= 0.277 Chirality : 0.037 0.159 1424 Planarity : 0.003 0.023 1509 Dihedral : 7.657 133.744 1262 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.45 % Allowed : 9.16 % Favored : 89.40 % 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: 2.71 (0.25), residues: 1139 helix: 3.35 (0.19), residues: 682 sheet: -0.06 (0.52), residues: 102 loop : -0.89 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.017 0.001 PHE C 291 TYR 0.012 0.001 TYR D 250 ARG 0.009 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7536 (mt-10) REVERT: B 101 MET cc_start: 0.8680 (mmm) cc_final: 0.8380 (mmt) REVERT: C 41 LYS cc_start: 0.8731 (tttt) cc_final: 0.8525 (ttmm) REVERT: D 223 ARG cc_start: 0.7443 (ttm-80) cc_final: 0.7229 (ttp-170) REVERT: D 306 MET cc_start: 0.6755 (tmm) cc_final: 0.6484 (tmm) REVERT: E 123 LEU cc_start: 0.9042 (tt) cc_final: 0.8546 (mt) REVERT: E 141 ARG cc_start: 0.7926 (mtp180) cc_final: 0.7605 (tpm170) REVERT: E 170 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8441 (tm-30) outliers start: 12 outliers final: 12 residues processed: 122 average time/residue: 0.5591 time to fit residues: 88.7846 Evaluate side-chains 123 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.0470 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 98 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8750 Z= 0.196 Angle : 0.502 6.111 11890 Z= 0.252 Chirality : 0.036 0.160 1424 Planarity : 0.003 0.023 1509 Dihedral : 7.228 133.641 1262 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.69 % Allowed : 9.04 % Favored : 89.28 % 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: 2.79 (0.25), residues: 1139 helix: 3.38 (0.19), residues: 684 sheet: -0.08 (0.52), residues: 102 loop : -0.80 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 298 HIS 0.003 0.001 HIS A 97 PHE 0.008 0.001 PHE A 32 TYR 0.010 0.001 TYR D 252 ARG 0.009 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 117 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7511 (mt-10) REVERT: B 101 MET cc_start: 0.8681 (mmm) cc_final: 0.8384 (mmt) REVERT: C 41 LYS cc_start: 0.8729 (tttt) cc_final: 0.8521 (ttmm) REVERT: D 306 MET cc_start: 0.6780 (tmm) cc_final: 0.6493 (tmm) REVERT: E 120 GLU cc_start: 0.8102 (tp30) cc_final: 0.7771 (tp30) REVERT: E 123 LEU cc_start: 0.9026 (tt) cc_final: 0.8533 (mt) REVERT: E 141 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7610 (tpm170) REVERT: E 170 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8435 (tm-30) outliers start: 14 outliers final: 13 residues processed: 125 average time/residue: 0.5408 time to fit residues: 88.8114 Evaluate side-chains 122 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 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 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8750 Z= 0.325 Angle : 0.551 6.163 11890 Z= 0.285 Chirality : 0.038 0.153 1424 Planarity : 0.003 0.025 1509 Dihedral : 7.312 140.273 1262 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.93 % Allowed : 9.64 % Favored : 88.43 % 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: 2.51 (0.25), residues: 1139 helix: 3.19 (0.19), residues: 682 sheet: -0.11 (0.57), residues: 82 loop : -0.94 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 298 HIS 0.004 0.001 HIS B 73 PHE 0.012 0.001 PHE A 32 TYR 0.012 0.002 TYR C 250 ARG 0.005 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 101 MET cc_start: 0.8701 (mmm) cc_final: 0.8431 (mmt) REVERT: C 41 LYS cc_start: 0.8774 (tttt) cc_final: 0.8547 (ttmm) REVERT: C 291 PHE cc_start: 0.7315 (t80) cc_final: 0.6750 (t80) REVERT: D 306 MET cc_start: 0.6895 (tmm) cc_final: 0.6550 (tmm) REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8546 (mt) REVERT: E 141 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7666 (tpm170) REVERT: E 170 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8444 (tm-30) outliers start: 16 outliers final: 14 residues processed: 125 average time/residue: 0.5067 time to fit residues: 83.4817 Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 111 GLN E 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8750 Z= 0.266 Angle : 0.527 6.104 11890 Z= 0.269 Chirality : 0.037 0.157 1424 Planarity : 0.003 0.025 1509 Dihedral : 7.292 144.484 1262 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.05 % Allowed : 9.88 % Favored : 88.07 % 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: 2.48 (0.25), residues: 1139 helix: 3.15 (0.19), residues: 684 sheet: -0.19 (0.56), residues: 82 loop : -0.94 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.010 0.001 PHE A 32 TYR 0.011 0.001 TYR C 250 ARG 0.003 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7619 (mt-10) REVERT: B 101 MET cc_start: 0.8691 (mmm) cc_final: 0.8399 (mmt) REVERT: C 41 LYS cc_start: 0.8767 (tttt) cc_final: 0.8552 (ttmm) REVERT: C 291 PHE cc_start: 0.7338 (t80) cc_final: 0.6809 (t80) REVERT: D 326 GLU cc_start: 0.8558 (pp20) cc_final: 0.8214 (pp20) REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8557 (mt) REVERT: E 141 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7653 (tpm170) REVERT: E 169 THR cc_start: 0.8134 (t) cc_final: 0.7933 (t) REVERT: E 170 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8420 (tm-30) outliers start: 17 outliers final: 13 residues processed: 125 average time/residue: 0.5315 time to fit residues: 87.8387 Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.7925 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8750 Z= 0.181 Angle : 0.503 6.288 11890 Z= 0.251 Chirality : 0.036 0.166 1424 Planarity : 0.003 0.028 1509 Dihedral : 7.178 145.667 1262 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.81 % Allowed : 10.72 % Favored : 87.47 % 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: 2.70 (0.25), residues: 1139 helix: 3.34 (0.19), residues: 681 sheet: -0.13 (0.57), residues: 82 loop : -0.83 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS A 97 PHE 0.008 0.001 PHE A 32 TYR 0.009 0.001 TYR D 252 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 129 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7594 (mt-10) REVERT: B 101 MET cc_start: 0.8677 (mmm) cc_final: 0.8384 (mmt) REVERT: C 41 LYS cc_start: 0.8745 (tttt) cc_final: 0.8528 (ttmm) REVERT: C 291 PHE cc_start: 0.7320 (t80) cc_final: 0.6795 (t80) REVERT: D 306 MET cc_start: 0.6700 (tmm) cc_final: 0.6437 (tmm) REVERT: D 326 GLU cc_start: 0.8594 (pp20) cc_final: 0.8226 (pp20) REVERT: E 119 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8215 (tp) REVERT: E 120 GLU cc_start: 0.8060 (tp30) cc_final: 0.7794 (tp30) REVERT: E 123 LEU cc_start: 0.9012 (tt) cc_final: 0.8553 (mt) REVERT: E 141 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7653 (tpm170) REVERT: E 167 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8436 (mm-30) REVERT: E 169 THR cc_start: 0.8112 (t) cc_final: 0.7908 (t) REVERT: E 170 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8403 (tm-30) outliers start: 15 outliers final: 13 residues processed: 122 average time/residue: 0.5168 time to fit residues: 83.8767 Evaluate side-chains 126 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8750 Z= 0.321 Angle : 0.553 6.058 11890 Z= 0.283 Chirality : 0.037 0.162 1424 Planarity : 0.003 0.030 1509 Dihedral : 7.368 149.748 1262 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.05 % Allowed : 11.20 % Favored : 86.75 % 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: 2.39 (0.25), residues: 1139 helix: 3.13 (0.19), residues: 681 sheet: -0.33 (0.55), residues: 82 loop : -1.02 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 298 HIS 0.004 0.001 HIS E 154 PHE 0.013 0.001 PHE A 32 TYR 0.012 0.002 TYR C 250 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7654 (mt-10) REVERT: B 101 MET cc_start: 0.8702 (mmm) cc_final: 0.8407 (mmt) REVERT: C 41 LYS cc_start: 0.8774 (tttt) cc_final: 0.8559 (ttmm) REVERT: C 291 PHE cc_start: 0.7355 (t80) cc_final: 0.6879 (t80) REVERT: D 306 MET cc_start: 0.6724 (tmm) cc_final: 0.6441 (tmm) REVERT: D 324 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8718 (mp) REVERT: D 326 GLU cc_start: 0.8641 (pp20) cc_final: 0.8296 (pp20) REVERT: E 123 LEU cc_start: 0.9015 (tt) cc_final: 0.8547 (mt) REVERT: E 141 ARG cc_start: 0.7974 (mtp180) cc_final: 0.7658 (tpm170) REVERT: E 167 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8437 (mm-30) REVERT: E 169 THR cc_start: 0.8120 (t) cc_final: 0.7918 (t) REVERT: E 170 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.5167 time to fit residues: 84.0449 Evaluate side-chains 126 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 102 optimal weight: 0.6980 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8750 Z= 0.200 Angle : 0.516 6.027 11890 Z= 0.259 Chirality : 0.036 0.168 1424 Planarity : 0.003 0.031 1509 Dihedral : 7.321 149.350 1262 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.69 % Allowed : 11.57 % Favored : 86.75 % 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: 2.58 (0.25), residues: 1139 helix: 3.26 (0.19), residues: 681 sheet: -0.19 (0.56), residues: 80 loop : -0.92 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.010 0.001 PHE A 32 TYR 0.010 0.001 TYR D 252 ARG 0.003 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8798 (mmtm) REVERT: C 41 LYS cc_start: 0.8758 (tttt) cc_final: 0.8549 (ttmm) REVERT: C 291 PHE cc_start: 0.7306 (t80) cc_final: 0.6807 (t80) REVERT: D 306 MET cc_start: 0.6711 (tmm) cc_final: 0.6429 (tmm) REVERT: D 326 GLU cc_start: 0.8640 (pp20) cc_final: 0.8291 (pp20) REVERT: E 119 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8257 (tp) REVERT: E 123 LEU cc_start: 0.9026 (tt) cc_final: 0.8580 (mt) REVERT: E 141 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7659 (tpm170) REVERT: E 170 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8403 (tm-30) outliers start: 14 outliers final: 12 residues processed: 121 average time/residue: 0.5272 time to fit residues: 84.9842 Evaluate side-chains 124 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.3980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 40.0000 chunk 104 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN E 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8750 Z= 0.271 Angle : 0.536 5.920 11890 Z= 0.272 Chirality : 0.037 0.170 1424 Planarity : 0.003 0.032 1509 Dihedral : 7.501 158.187 1262 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.81 % Allowed : 11.45 % Favored : 86.75 % 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: 2.45 (0.25), residues: 1139 helix: 3.19 (0.19), residues: 681 sheet: -0.26 (0.56), residues: 80 loop : -1.03 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.011 0.001 PHE A 32 TYR 0.011 0.001 TYR D 250 ARG 0.005 0.000 ARG C 50 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue SER 46 is missing expected H atoms. Skipping. Residue SER 51 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 111 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue THR 149 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue MET 184 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 92 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue VAL 106 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue LYS 119 is missing expected H atoms. Skipping. Residue LYS 121 is missing expected H atoms. Skipping. Residue SER 124 is missing expected H atoms. Skipping. Residue VAL 153 is missing expected H atoms. Skipping. Residue VAL 155 is missing expected H atoms. Skipping. Residue VAL 156 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LYS 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue SER 162 is missing expected H atoms. Skipping. Residue ILE 166 is missing expected H atoms. Skipping. Residue THR 168 is missing expected H atoms. Skipping. Residue LYS 171 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue ILE 294 is missing expected H atoms. Skipping. Residue LEU 91 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LEU 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 110 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue SER 175 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 182 is missing expected H atoms. Skipping. Residue ILE 187 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue LEU 190 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.9055 (mmtm) cc_final: 0.8815 (mmtm) REVERT: A 61 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 41 LYS cc_start: 0.8763 (tttt) cc_final: 0.8552 (ttmm) REVERT: C 291 PHE cc_start: 0.7350 (t80) cc_final: 0.6916 (t80) REVERT: D 306 MET cc_start: 0.6712 (tmm) cc_final: 0.6429 (tmm) REVERT: D 326 GLU cc_start: 0.8663 (pp20) cc_final: 0.8319 (pp20) REVERT: E 119 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8216 (tp) REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8554 (mt) REVERT: E 141 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7663 (tpm170) REVERT: E 170 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 15 outliers final: 12 residues processed: 120 average time/residue: 0.5203 time to fit residues: 83.4494 Evaluate side-chains 125 residues out of total 973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 176 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 149 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 79 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.084914 restraints weight = 48721.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088909 restraints weight = 20157.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091515 restraints weight = 11303.153| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8750 Z= 0.244 Angle : 0.526 5.809 11890 Z= 0.267 Chirality : 0.036 0.167 1424 Planarity : 0.003 0.030 1509 Dihedral : 7.704 169.796 1262 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.57 % Allowed : 11.69 % Favored : 86.75 % 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: 2.45 (0.25), residues: 1139 helix: 3.21 (0.19), residues: 681 sheet: -0.37 (0.55), residues: 80 loop : -1.05 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 298 HIS 0.003 0.001 HIS A 33 PHE 0.011 0.001 PHE A 32 TYR 0.010 0.001 TYR C 250 ARG 0.006 0.000 ARG C 50 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3821.49 seconds wall clock time: 67 minutes 17.60 seconds (4037.60 seconds total)