Starting phenix.real_space_refine on Tue Feb 13 20:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6d_25713/02_2024/7t6d_25713_updated.pdb" } resolution = 3.9 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= 0.008 sd= 0.059 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 4842 2.51 5 N 1362 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "B GLU 70": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7566 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2185 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 2181 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 382} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1230 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 25, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 588 Conformer: "B" Number of residues, atoms: 389, 2181 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 382} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1230 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 19, 'ASP:plan': 25, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 4, 'HIS:plan': 7, 'PHE:plan': 6, 'GLU:plan': 30, 'ARG:plan': 25} Unresolved non-hydrogen planarities: 588 bond proxies already assigned to first conformer: 2188 Chain: "B" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2404 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 5, 'TRANS': 375} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 414 Conformer: "B" Number of residues, atoms: 381, 2404 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 5, 'TRANS': 375} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 4, 'TYR:plan': 6, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 21, 'PHE:plan': 2, 'GLU:plan': 24, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 414 bond proxies already assigned to first conformer: 2428 Chain: "C" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1544 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1336 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 86} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 2, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 196 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.26, per 1000 atoms: 0.96 Number of scatterers: 7566 At special positions: 0 Unit cell: (91.528, 114.41, 162.866, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 2 15.00 O 1339 8.00 N 1362 7.00 C 4842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 3.0 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 2 sheets defined 76.0% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 3 through 47 removed outlier: 4.187A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 51 through 62 removed outlier: 3.712A pdb=" N ASP A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 103 through 120 Processing helix chain 'A' and resid 123 through 133 removed outlier: 4.095A pdb=" N GLN A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 154 removed outlier: 3.535A pdb=" N ARG A 140 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE A 141 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY A 142 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 154 " --> pdb=" O TYR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 175 through 189 Processing helix chain 'A' and resid 196 through 209 removed outlier: 3.937A pdb=" N THR A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 231 through 243 removed outlier: 4.015A pdb=" N ILE A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 removed outlier: 4.065A pdb=" N SER A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN A 261 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 276 Processing helix chain 'A' and resid 282 through 296 Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 333 through 351 Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.280A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 37 through 47 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 70 through 81 Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 103 through 120 Processing helix chain 'B' and resid 123 through 133 removed outlier: 4.189A pdb=" N GLN B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 153 Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 176 through 194 removed outlier: 4.313A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 231 through 243 removed outlier: 4.296A pdb=" N VAL B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 262 removed outlier: 3.821A pdb=" N LEU B 252 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN B 261 " --> pdb=" O CYS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 278 removed outlier: 3.694A pdb=" N GLU B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 334 through 351 Processing helix chain 'C' and resid 4 through 40 removed outlier: 3.593A pdb=" N VAL C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 79 removed outlier: 4.491A pdb=" N PHE C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Proline residue: C 75 - end of helix removed outlier: 3.982A pdb=" N PHE C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE C 79 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 111 Processing helix chain 'C' and resid 117 through 123 Processing helix chain 'C' and resid 134 through 158 Proline residue: C 143 - end of helix Processing helix chain 'C' and resid 160 through 193 removed outlier: 5.690A pdb=" N ARG C 168 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N PHE C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) Proline residue: C 172 - end of helix Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'D' and resid 6 through 40 removed outlier: 3.593A pdb=" N VAL D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 79 removed outlier: 4.490A pdb=" N PHE D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Proline residue: D 75 - end of helix removed outlier: 3.982A pdb=" N PHE D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE D 79 " --> pdb=" O PRO D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 111 Processing helix chain 'D' and resid 117 through 123 Processing helix chain 'D' and resid 134 through 158 Proline residue: D 143 - end of helix Processing helix chain 'D' and resid 160 through 193 removed outlier: 5.691A pdb=" N ARG D 168 " --> pdb=" O THR D 164 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 198 through 202 Processing sheet with id= A, first strand: chain 'A' and resid 355 through 357 Processing sheet with id= B, first strand: chain 'B' and resid 355 through 357 removed outlier: 3.642A pdb=" N LYS B 381 " --> pdb=" O ARG B 356 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1787 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1253 1.32 - 1.44: 1980 1.44 - 1.57: 4401 1.57 - 1.69: 3 1.69 - 1.81: 41 Bond restraints: 7678 Sorted by residual: bond pdb=" C LEU B 8 " pdb=" N LEU B 9 " ideal model delta sigma weight residual 1.332 1.387 -0.055 1.50e-02 4.44e+03 1.33e+01 bond pdb=" C VAL D 32 " pdb=" O VAL D 32 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C VAL C 32 " pdb=" O VAL C 32 " ideal model delta sigma weight residual 1.237 1.277 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" C6 LPP A 401 " pdb=" O5 LPP A 401 " ideal model delta sigma weight residual 1.399 1.466 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C29 LPP A 401 " pdb=" O27 LPP A 401 " ideal model delta sigma weight residual 1.399 1.332 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 95.88 - 103.51: 51 103.51 - 111.14: 3062 111.14 - 118.77: 3074 118.77 - 126.40: 4261 126.40 - 134.03: 80 Bond angle restraints: 10528 Sorted by residual: angle pdb=" N PRO C 211 " pdb=" CA PRO C 211 " pdb=" CB PRO C 211 " ideal model delta sigma weight residual 103.25 95.88 7.37 1.05e+00 9.07e-01 4.93e+01 angle pdb=" N GLY B 67 " pdb=" CA GLY B 67 " pdb=" C GLY B 67 " ideal model delta sigma weight residual 115.36 107.52 7.84 1.33e+00 5.65e-01 3.47e+01 angle pdb=" C LEU B 8 " pdb=" N LEU B 9 " pdb=" CA LEU B 9 " ideal model delta sigma weight residual 120.26 113.87 6.39 1.34e+00 5.57e-01 2.28e+01 angle pdb=" CA THR B 68 " pdb=" C THR B 68 " pdb=" O THR B 68 " ideal model delta sigma weight residual 122.64 117.60 5.04 1.25e+00 6.40e-01 1.62e+01 angle pdb=" N LEU A 8 " pdb=" CA LEU A 8 " pdb=" C LEU A 8 " ideal model delta sigma weight residual 111.28 115.61 -4.33 1.09e+00 8.42e-01 1.58e+01 ... (remaining 10523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 4290 23.13 - 46.27: 159 46.27 - 69.40: 28 69.40 - 92.53: 5 92.53 - 115.66: 1 Dihedral angle restraints: 4483 sinusoidal: 1021 harmonic: 3462 Sorted by residual: dihedral pdb=" CD ARG C 161 " pdb=" NE ARG C 161 " pdb=" CZ ARG C 161 " pdb=" NH1 ARG C 161 " ideal model delta sinusoidal sigma weight residual 0.00 82.22 -82.22 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" C TYR D 210 " pdb=" N TYR D 210 " pdb=" CA TYR D 210 " pdb=" CB TYR D 210 " ideal model delta harmonic sigma weight residual -122.60 -110.64 -11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" C TYR C 210 " pdb=" N TYR C 210 " pdb=" CA TYR C 210 " pdb=" CB TYR C 210 " ideal model delta harmonic sigma weight residual -122.60 -110.67 -11.93 0 2.50e+00 1.60e-01 2.28e+01 ... (remaining 4480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1182 0.074 - 0.147: 109 0.147 - 0.221: 13 0.221 - 0.294: 2 0.294 - 0.368: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU A 2 " pdb=" N LEU A 2 " pdb=" C LEU A 2 " pdb=" CB LEU A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA LEU B 2 " pdb=" N LEU B 2 " pdb=" C LEU B 2 " pdb=" CB LEU B 2 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TYR D 210 " pdb=" N TYR D 210 " pdb=" C TYR D 210 " pdb=" CB TYR D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 1307 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PGV C 601 " 0.222 2.00e-02 2.50e+03 2.18e-01 4.77e+02 pdb=" C11 PGV C 601 " -0.234 2.00e-02 2.50e+03 pdb=" C12 PGV C 601 " -0.202 2.00e-02 2.50e+03 pdb=" C13 PGV C 601 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 161 " -1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG C 161 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 161 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 161 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 161 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 22 " -0.371 9.50e-02 1.11e+02 1.66e-01 1.70e+01 pdb=" NE ARG A 22 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 22 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 22 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 22 " -0.013 2.00e-02 2.50e+03 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 214 2.72 - 3.26: 8070 3.26 - 3.81: 12512 3.81 - 4.35: 13081 4.35 - 4.90: 22487 Nonbonded interactions: 56364 Sorted by model distance: nonbonded pdb=" O LEU A 2 " pdb=" CD2 PHE A 6 " model vdw 2.172 3.340 nonbonded pdb=" O VAL D 16 " pdb=" ND1 HIS D 20 " model vdw 2.177 2.520 nonbonded pdb=" NE ARG A 22 " pdb=" O2 LPP A 401 " model vdw 2.219 2.520 nonbonded pdb=" CZ ARG A 22 " pdb=" O2 LPP A 401 " model vdw 2.220 3.270 nonbonded pdb=" NH1 ARG A 37 " pdb=" OD2 ASP B 138 " model vdw 2.239 2.520 ... (remaining 56359 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' and (resid 1 through 27 or resid 36 or (resid 37 through 38 and (name \ N or name CA or name C or name O or name CB )) or resid 39 through 60 or (resid \ 61 through 66 and (name N or name CA or name C or name O or name CB )) or resid \ 67 through 114 or (resid 115 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE )) or resid 116 through 121 or (resid 122 t \ hrough 128 and (name N or name CA or name C or name O or name CB )) or resid 129 \ through 235 or resid 237 through 266 or resid 268 through 389)) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 54 or (resid 55 through 56 and (name N or name CA \ or name C or name O or name CB )) or resid 57 through 58 or (resid 59 through 6 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 67 or (resid \ 68 through 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 92 or (resid 93 through 106 and (name N or name CA or name C or name \ O or name CB )) or resid 107 through 122 or (resid 123 through 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 through 133 or (resid \ 134 through 141 and (name N or name CA or name C or name O or name CB )) or (res \ id 142 through 145 and (name N or name CA or name C or name O or name CB )) or r \ esid 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 153 or (resid 154 through 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 or (resid 172 through 205 and (name N o \ r name CA or name C or name O or name CB )) or (resid 206 through 220 and (name \ N or name CA or name C or name O or name CB )) or resid 221 or (resid 222 throug \ h 227 and (name N or name CA or name C or name O or name CB )) or (resid 228 thr \ ough 235 and (name N or name CA or name C or name O or name CB )) or (resid 237 \ through 262 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 3 through 266 or (resid 268 through 280 and (name N or name CA or name C or name \ O or name CB )) or resid 281 through 389)) } ncs_group { reference = (chain 'C' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 28 or (resid 29 through 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 90 or (resid 91 through 92 and (name N or name CA or name C or name O or name \ CB )) or resid 93 through 94 or (resid 95 through 96 and (name N or name CA or \ name C or name O or name CB )) or resid 97 through 101 or (resid 102 through 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 1 \ 13 or (resid 114 through 123 and (name N or name CA or name C or name O or name \ CB )) or (resid 124 and (name N or name CA or name C or name O )) or (resid 133 \ through 144 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 5 through 148 or (resid 149 through 151 and (name N or name CA or name C or name \ O or name CB )) or resid 152 through 153 or (resid 154 and (name N or name CA o \ r name C or name O or name CB )) or resid 155 through 160 or (resid 161 through \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 throug \ h 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 200 or (resid 201 through 202 and (name N or name CA or name C \ or name O or name CB )) or resid 203 through 210)) selection = (chain 'D' and (resid 5 through 82 or (resid 83 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 210)) } 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.960 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 29.510 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 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 : 0.006 0.067 7678 Z= 0.390 Angle : 0.843 9.627 10528 Z= 0.542 Chirality : 0.051 0.368 1310 Planarity : 0.016 0.488 1369 Dihedral : 13.505 115.664 2227 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 1.42 % Allowed : 1.42 % Favored : 97.16 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1170 helix: 1.38 (0.17), residues: 924 sheet: -2.39 (1.21), residues: 20 loop : -1.43 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 18 HIS 0.007 0.001 HIS C 4 PHE 0.017 0.001 PHE A 45 TYR 0.020 0.002 TYR C 210 ARG 0.002 0.000 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 0.954 Fit side-chains REVERT: B 45 PHE cc_start: 0.7963 (m-80) cc_final: 0.7703 (m-80) REVERT: C 27 ILE cc_start: 0.7613 (tt) cc_final: 0.7366 (tt) REVERT: C 159 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8779 (tppt) REVERT: C 168 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8088 (ttp80) REVERT: D 18 TRP cc_start: 0.6662 (t60) cc_final: 0.5967 (t60) REVERT: D 27 ILE cc_start: 0.7398 (tt) cc_final: 0.7097 (tt) REVERT: D 172 PRO cc_start: 0.7242 (Cg_exo) cc_final: 0.6816 (Cg_endo) outliers start: 6 outliers final: 2 residues processed: 174 average time/residue: 0.1967 time to fit residues: 45.7025 Evaluate side-chains 126 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain C residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 30 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 181 HIS C 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 7678 Z= 0.229 Angle : 0.548 8.151 10528 Z= 0.291 Chirality : 0.037 0.247 1310 Planarity : 0.005 0.107 1369 Dihedral : 9.236 114.312 1319 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.06 % Favored : 97.86 % Rotamer: Outliers : 2.13 % Allowed : 16.08 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1170 helix: 1.88 (0.17), residues: 918 sheet: -1.74 (1.49), residues: 15 loop : -1.07 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 PHE 0.036 0.002 PHE A 6 TYR 0.019 0.002 TYR B 117 ARG 0.005 0.001 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 126 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: C 36 ARG cc_start: 0.8353 (ttt180) cc_final: 0.8028 (ttt90) REVERT: C 155 TRP cc_start: 0.8772 (t60) cc_final: 0.8205 (t60) REVERT: C 159 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8701 (tppt) REVERT: C 168 ARG cc_start: 0.8581 (ttp-110) cc_final: 0.8370 (ttp80) REVERT: D 18 TRP cc_start: 0.6626 (t60) cc_final: 0.6159 (t60) REVERT: D 27 ILE cc_start: 0.7377 (tt) cc_final: 0.7134 (tt) REVERT: D 99 THR cc_start: 0.7302 (p) cc_final: 0.6904 (p) outliers start: 9 outliers final: 7 residues processed: 132 average time/residue: 0.1765 time to fit residues: 31.9977 Evaluate side-chains 124 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 40.0000 chunk 105 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7678 Z= 0.269 Angle : 0.563 12.028 10528 Z= 0.296 Chirality : 0.037 0.189 1310 Planarity : 0.005 0.118 1369 Dihedral : 8.761 136.011 1318 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 3.55 % Allowed : 16.78 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 2.10 (0.25), residues: 1170 helix: 1.99 (0.17), residues: 927 sheet: -1.69 (2.01), residues: 10 loop : -0.91 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 18 HIS 0.007 0.002 HIS D 20 PHE 0.017 0.002 PHE C 22 TYR 0.020 0.002 TYR B 117 ARG 0.004 0.001 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 0.878 Fit side-chains REVERT: A 44 ASN cc_start: 0.8234 (t0) cc_final: 0.7847 (t0) REVERT: A 112 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8640 (tp40) REVERT: B 74 THR cc_start: 0.9354 (m) cc_final: 0.9099 (m) REVERT: C 36 ARG cc_start: 0.8570 (ttt180) cc_final: 0.7877 (ttt180) REVERT: C 155 TRP cc_start: 0.8812 (t60) cc_final: 0.8192 (t60) REVERT: C 159 LYS cc_start: 0.9039 (mmtm) cc_final: 0.8719 (tppt) REVERT: D 18 TRP cc_start: 0.6727 (t60) cc_final: 0.6221 (t60) REVERT: D 99 THR cc_start: 0.7730 (p) cc_final: 0.7417 (p) outliers start: 15 outliers final: 10 residues processed: 128 average time/residue: 0.1760 time to fit residues: 31.1940 Evaluate side-chains 122 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 70 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7678 Z= 0.308 Angle : 0.557 7.122 10528 Z= 0.298 Chirality : 0.037 0.164 1310 Planarity : 0.004 0.060 1369 Dihedral : 8.881 146.350 1314 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.55 % Allowed : 18.91 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.17 (0.25), residues: 1170 helix: 1.99 (0.17), residues: 924 sheet: -3.04 (2.74), residues: 5 loop : -0.62 (0.41), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 18 HIS 0.006 0.001 HIS C 60 PHE 0.016 0.002 PHE D 176 TYR 0.016 0.002 TYR B 117 ARG 0.003 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 0.973 Fit side-chains REVERT: A 44 ASN cc_start: 0.8273 (t0) cc_final: 0.7920 (t0) REVERT: B 7 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8043 (tp) REVERT: B 74 THR cc_start: 0.9333 (m) cc_final: 0.9074 (m) REVERT: B 135 ASP cc_start: 0.8086 (t0) cc_final: 0.7376 (m-30) REVERT: C 105 SER cc_start: 0.8105 (m) cc_final: 0.7875 (p) REVERT: C 155 TRP cc_start: 0.8829 (t60) cc_final: 0.8226 (t60) REVERT: C 159 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8672 (tppt) REVERT: D 18 TRP cc_start: 0.6782 (t60) cc_final: 0.6233 (t60) REVERT: D 61 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.6098 (t80) outliers start: 15 outliers final: 8 residues processed: 124 average time/residue: 0.1486 time to fit residues: 27.0203 Evaluate side-chains 125 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 83 optimal weight: 0.2980 chunk 46 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 28 optimal weight: 5.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS C 202 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7678 Z= 0.155 Angle : 0.469 7.585 10528 Z= 0.248 Chirality : 0.034 0.167 1310 Planarity : 0.003 0.062 1369 Dihedral : 8.476 144.917 1314 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.13 % Allowed : 23.40 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.52 (0.25), residues: 1170 helix: 2.24 (0.17), residues: 933 sheet: -2.86 (1.66), residues: 10 loop : -0.56 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 18 HIS 0.002 0.001 HIS B 72 PHE 0.014 0.001 PHE C 61 TYR 0.011 0.001 TYR C 188 ARG 0.003 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: B 74 THR cc_start: 0.9318 (m) cc_final: 0.9052 (m) REVERT: C 36 ARG cc_start: 0.8198 (ttt180) cc_final: 0.7698 (ttt90) REVERT: C 155 TRP cc_start: 0.8779 (t60) cc_final: 0.8205 (t60) REVERT: C 159 LYS cc_start: 0.8970 (mmtm) cc_final: 0.8664 (tppt) REVERT: D 61 PHE cc_start: 0.6375 (OUTLIER) cc_final: 0.5787 (t80) outliers start: 9 outliers final: 4 residues processed: 126 average time/residue: 0.1545 time to fit residues: 28.0833 Evaluate side-chains 120 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7678 Z= 0.199 Angle : 0.488 7.947 10528 Z= 0.258 Chirality : 0.035 0.176 1310 Planarity : 0.003 0.064 1369 Dihedral : 8.479 147.065 1314 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.60 % Allowed : 24.35 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.53 (0.25), residues: 1170 helix: 2.27 (0.17), residues: 933 sheet: -1.50 (1.39), residues: 15 loop : -0.68 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 PHE 0.015 0.002 PHE D 22 TYR 0.010 0.001 TYR C 52 ARG 0.002 0.000 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: B 74 THR cc_start: 0.9334 (m) cc_final: 0.9070 (m) REVERT: B 118 MET cc_start: 0.8737 (ttm) cc_final: 0.8471 (ttp) REVERT: B 135 ASP cc_start: 0.8037 (t0) cc_final: 0.7254 (m-30) REVERT: C 155 TRP cc_start: 0.8823 (t60) cc_final: 0.8207 (t60) REVERT: C 159 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8591 (tppt) REVERT: D 61 PHE cc_start: 0.6434 (OUTLIER) cc_final: 0.5892 (t80) outliers start: 11 outliers final: 9 residues processed: 118 average time/residue: 0.1504 time to fit residues: 26.2186 Evaluate side-chains 117 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0970 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6292 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7678 Z= 0.163 Angle : 0.499 9.713 10528 Z= 0.255 Chirality : 0.035 0.178 1310 Planarity : 0.003 0.060 1369 Dihedral : 8.340 146.877 1314 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.84 % Allowed : 25.53 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.63 (0.25), residues: 1170 helix: 2.32 (0.17), residues: 935 sheet: -1.33 (1.42), residues: 15 loop : -0.61 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 PHE 0.013 0.001 PHE C 61 TYR 0.010 0.001 TYR A 117 ARG 0.002 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.813 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.7942 (t0) cc_final: 0.7564 (t0) REVERT: B 74 THR cc_start: 0.9312 (m) cc_final: 0.9048 (m) REVERT: B 118 MET cc_start: 0.8640 (ttm) cc_final: 0.8342 (ttp) REVERT: C 36 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7470 (ttt90) REVERT: C 155 TRP cc_start: 0.8784 (t60) cc_final: 0.8194 (t60) REVERT: C 159 LYS cc_start: 0.8956 (mmtm) cc_final: 0.8589 (tppt) REVERT: D 61 PHE cc_start: 0.6341 (OUTLIER) cc_final: 0.5856 (t80) outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.1552 time to fit residues: 26.3641 Evaluate side-chains 117 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 0.0170 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 HIS ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7678 Z= 0.397 Angle : 0.664 10.839 10528 Z= 0.347 Chirality : 0.040 0.195 1310 Planarity : 0.004 0.058 1369 Dihedral : 8.894 156.303 1314 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.84 % Allowed : 26.48 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.15 (0.25), residues: 1170 helix: 1.96 (0.17), residues: 930 sheet: -1.54 (1.42), residues: 15 loop : -0.55 (0.43), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 18 HIS 0.009 0.002 HIS C 60 PHE 0.018 0.002 PHE D 63 TYR 0.019 0.002 TYR B 117 ARG 0.005 0.001 ARG A 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.8026 (t0) cc_final: 0.7432 (t0) REVERT: B 39 TYR cc_start: 0.8627 (m-10) cc_final: 0.8296 (m-10) REVERT: B 135 ASP cc_start: 0.8165 (t0) cc_final: 0.7430 (m-30) REVERT: C 155 TRP cc_start: 0.8844 (t60) cc_final: 0.8235 (t60) REVERT: C 159 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8625 (tppt) REVERT: D 61 PHE cc_start: 0.6663 (OUTLIER) cc_final: 0.6342 (t80) outliers start: 12 outliers final: 5 residues processed: 120 average time/residue: 0.1551 time to fit residues: 27.5228 Evaluate side-chains 113 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 110 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 ASN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6335 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7678 Z= 0.171 Angle : 0.531 10.427 10528 Z= 0.269 Chirality : 0.035 0.198 1310 Planarity : 0.003 0.051 1369 Dihedral : 8.423 152.683 1314 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.13 % Allowed : 26.71 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.55 (0.25), residues: 1170 helix: 2.26 (0.17), residues: 925 sheet: -1.32 (1.42), residues: 15 loop : -0.47 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 PHE 0.019 0.002 PHE D 22 TYR 0.012 0.001 TYR C 52 ARG 0.009 0.000 ARG D 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.8041 (t0) cc_final: 0.7665 (t0) REVERT: B 135 ASP cc_start: 0.8192 (t0) cc_final: 0.7535 (m-30) REVERT: B 170 LEU cc_start: 0.8804 (tp) cc_final: 0.8519 (tp) REVERT: C 155 TRP cc_start: 0.8786 (t60) cc_final: 0.8230 (t60) REVERT: C 159 LYS cc_start: 0.8881 (mmtm) cc_final: 0.8527 (tppt) REVERT: D 22 PHE cc_start: 0.5078 (t80) cc_final: 0.4864 (t80) outliers start: 9 outliers final: 6 residues processed: 123 average time/residue: 0.1511 time to fit residues: 27.0450 Evaluate side-chains 120 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 37 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 92 optimal weight: 0.0370 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 26 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7678 Z= 0.285 Angle : 0.586 10.124 10528 Z= 0.300 Chirality : 0.037 0.207 1310 Planarity : 0.003 0.053 1369 Dihedral : 8.505 155.031 1314 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 26.95 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1170 helix: 2.18 (0.17), residues: 931 sheet: -1.40 (1.43), residues: 15 loop : -0.40 (0.44), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 18 HIS 0.006 0.001 HIS D 60 PHE 0.017 0.002 PHE D 22 TYR 0.013 0.001 TYR B 117 ARG 0.005 0.001 ARG D 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 112 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 44 ASN cc_start: 0.8082 (t0) cc_final: 0.7698 (t0) REVERT: B 135 ASP cc_start: 0.8179 (t0) cc_final: 0.7432 (m-30) REVERT: C 155 TRP cc_start: 0.8837 (t60) cc_final: 0.8257 (t60) REVERT: C 159 LYS cc_start: 0.8917 (mmtm) cc_final: 0.8560 (tppt) REVERT: D 22 PHE cc_start: 0.4941 (t80) cc_final: 0.4627 (t80) outliers start: 8 outliers final: 4 residues processed: 115 average time/residue: 0.1489 time to fit residues: 25.4283 Evaluate side-chains 115 residues out of total 1009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain D residue 10 GLU Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 94 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.212510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.197583 restraints weight = 22438.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.196005 restraints weight = 19974.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.194696 restraints weight = 11864.422| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4240 r_free = 0.4240 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 7678 Z= 0.342 Angle : 0.636 13.781 10528 Z= 0.325 Chirality : 0.038 0.199 1310 Planarity : 0.003 0.049 1369 Dihedral : 8.612 156.988 1314 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.89 % Allowed : 26.48 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.31 (0.25), residues: 1170 helix: 2.03 (0.17), residues: 929 sheet: -1.36 (1.44), residues: 15 loop : -0.31 (0.45), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 18 HIS 0.007 0.002 HIS C 60 PHE 0.018 0.002 PHE D 22 TYR 0.014 0.002 TYR B 117 ARG 0.006 0.001 ARG D 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1525.31 seconds wall clock time: 28 minutes 12.27 seconds (1692.27 seconds total)