Starting phenix.real_space_refine on Mon Feb 19 01:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/02_2024/7nst_12576.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 S 22 5.16 5 C 8117 2.51 5 N 2210 2.21 5 O 2597 1.98 5 H 10582 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23528 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5071 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "B" Number of atoms: 5071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5071 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "C" Number of atoms: 5068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5068 Classifications: {'peptide': 340} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 335} Chain: "D" Number of atoms: 2317 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 289, 2306 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 22, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 289, 2306 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 22, 'TRANS': 266} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 2332 Chain: "E" Number of atoms: 6001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 5857 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 26, 'TRANS': 367} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 5857 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 26, 'TRANS': 367} Chain breaks: 1 bond proxies already assigned to first conformer: 5773 Time building chain proxies: 14.22, per 1000 atoms: 0.60 Number of scatterers: 23528 At special positions: 0 Unit cell: (181.131, 104.7, 93.183, 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 22 16.00 O 2597 8.00 N 2210 7.00 C 8117 6.00 H 10582 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: 19.04 Conformation dependent library (CDL) restraints added in 3.8 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2980 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 10.2% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.816A pdb=" N ASP A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 197 through 203 removed outlier: 3.504A pdb=" N GLN A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.816A pdb=" N ASP B 107 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.505A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 removed outlier: 3.815A pdb=" N ASP C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C 111 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.504A pdb=" N GLN C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 125 removed outlier: 3.521A pdb=" N LYS D 125 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 3.908A pdb=" N LYS D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.893A pdb=" N GLY D 280 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 314 Processing helix chain 'E' and resid 53 through 65 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.685A pdb=" N TRP E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 140 through 158 Processing helix chain 'E' and resid 394 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2 through 6 current: chain 'A' and resid 55 through 66 removed outlier: 6.560A pdb=" N ASN A 64 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR A 81 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN A 101 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY A 134 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 292 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA A 280 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP A 290 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP A 282 " --> pdb=" O ASP A 288 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASP A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 2 through 6 current: chain 'B' and resid 55 through 66 removed outlier: 6.561A pdb=" N ASN B 64 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR B 81 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN B 101 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLY B 134 " --> pdb=" O ASN B 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 292 " --> pdb=" O SER B 278 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA B 280 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ASP B 290 " --> pdb=" O ALA B 280 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP B 282 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP B 288 " --> pdb=" O ASP B 282 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N MET B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 6 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 2 through 6 current: chain 'C' and resid 55 through 66 removed outlier: 6.560A pdb=" N ASN C 64 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR C 81 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C 101 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLY C 134 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 292 " --> pdb=" O SER C 278 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 280 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ASP C 290 " --> pdb=" O ALA C 280 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP C 282 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP C 288 " --> pdb=" O ASP C 282 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N MET C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'D' and resid 94 through 96 removed outlier: 19.651A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 14.062A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY D 202 " --> pdb=" O ASN D 183 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ASN D 183 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N ASN D 181 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER D 206 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR D 179 " --> pdb=" O SER D 206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 94 through 96 removed outlier: 19.651A pdb=" N THR D 268 " --> pdb=" O GLY D 202 " (cutoff:3.500A) removed outlier: 14.062A pdb=" N ASP D 270 " --> pdb=" O PRO D 204 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N SER D 206 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N VAL D 272 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ARG D 274 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL D 210 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN D 195 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N SER D 139 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 197 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 104 removed outlier: 6.439A pdb=" N LEU D 103 " --> pdb=" O ASN D 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 68 through 70 removed outlier: 9.224A pdb=" N VAL E 100 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N GLY E 38 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N GLY E 102 " --> pdb=" O GLY E 38 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR E 112 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL E 114 " --> pdb=" O SER E 133 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER E 133 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR E 116 " --> pdb=" O GLN E 131 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN E 131 " --> pdb=" O TYR E 116 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU E 118 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 193 through 198 removed outlier: 6.573A pdb=" N LEU E 182 " --> pdb=" O VAL E 195 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG E 197 " --> pdb=" O TYR E 180 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR E 180 " --> pdb=" O ARG E 197 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL E 170 " --> pdb=" O PHE E 423 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE E 423 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN E 172 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL E 421 " --> pdb=" O GLN E 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 202 through 207 removed outlier: 5.640A pdb=" N SER E 204 " --> pdb=" O VAL E 217 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL E 217 " --> pdb=" O SER E 204 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 226 " --> pdb=" O VAL E 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251 removed outlier: 5.790A pdb=" N ALA E 248 " --> pdb=" O ALA E 261 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA E 261 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 291 through 295 removed outlier: 6.490A pdb=" N ALA E 303 " --> pdb=" O PRO E 293 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TRP E 295 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASN E 301 " --> pdb=" O TRP E 295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 333 through 339 removed outlier: 4.314A pdb=" N ALA E 337 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL E 347 " --> pdb=" O ALA E 337 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL E 339 " --> pdb=" O PHE E 345 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE E 345 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 378 through 382 removed outlier: 6.327A pdb=" N ILE E 390 " --> pdb=" O PRO E 380 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU E 382 " --> pdb=" O MET E 388 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET E 388 " --> pdb=" O LEU E 382 " (cutoff:3.500A) 580 hydrogen bonds defined for protein. 1575 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: 9.19 Time building geometry restraints manager: 19.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.01: 10580 1.01 - 1.22: 3 1.22 - 1.43: 5948 1.43 - 1.65: 7244 1.65 - 1.86: 42 Bond restraints: 23817 Sorted by residual: bond pdb=" ND2 ASN E 290 " pdb="HD22 ASN E 290 " ideal model delta sigma weight residual 0.860 0.794 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" N ILE D 54 " pdb=" H ILE D 54 " ideal model delta sigma weight residual 0.860 0.916 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" N GLY D 58 " pdb=" H GLY D 58 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.76e+00 bond pdb=" N GLY D 57 " pdb=" H GLY D 57 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" N HIS D 55 " pdb=" H HIS D 55 " ideal model delta sigma weight residual 0.860 0.909 -0.049 2.00e-02 2.50e+03 5.94e+00 ... (remaining 23812 not shown) Histogram of bond angle deviations from ideal: 77.50 - 89.42: 8 89.42 - 101.33: 19 101.33 - 113.25: 25422 113.25 - 125.17: 16088 125.17 - 137.08: 325 Bond angle restraints: 41862 Sorted by residual: angle pdb="HD22 LEU A 88 " pdb=" CD2 LEU A 88 " pdb="HD23 LEU A 88 " ideal model delta sigma weight residual 110.00 77.50 32.50 3.00e+00 1.11e-01 1.17e+02 angle pdb="HD21 LEU A 88 " pdb=" CD2 LEU A 88 " pdb="HD22 LEU A 88 " ideal model delta sigma weight residual 110.00 77.70 32.30 3.00e+00 1.11e-01 1.16e+02 angle pdb="HD11 LEU A 88 " pdb=" CD1 LEU A 88 " pdb="HD12 LEU A 88 " ideal model delta sigma weight residual 110.00 78.93 31.07 3.00e+00 1.11e-01 1.07e+02 angle pdb="HD12 LEU A 88 " pdb=" CD1 LEU A 88 " pdb="HD13 LEU A 88 " ideal model delta sigma weight residual 110.00 81.00 29.00 3.00e+00 1.11e-01 9.35e+01 angle pdb=" CG LEU A 88 " pdb=" CD1 LEU A 88 " pdb="HD11 LEU A 88 " ideal model delta sigma weight residual 109.00 80.48 28.52 3.00e+00 1.11e-01 9.04e+01 ... (remaining 41857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 10501 17.81 - 35.62: 819 35.62 - 53.43: 222 53.43 - 71.24: 81 71.24 - 89.04: 9 Dihedral angle restraints: 11632 sinusoidal: 5942 harmonic: 5690 Sorted by residual: dihedral pdb=" CA MET E 203 " pdb=" C MET E 203 " pdb=" N SER E 204 " pdb=" CA SER E 204 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU E 302 " pdb=" C LEU E 302 " pdb=" N ALA E 303 " pdb=" CA ALA E 303 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ASP A 127 " pdb=" C ASP A 127 " pdb=" N PHE A 128 " pdb=" CA PHE A 128 " ideal model delta harmonic sigma weight residual 180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 11629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1411 0.043 - 0.085: 322 0.085 - 0.128: 137 0.128 - 0.171: 13 0.171 - 0.214: 2 Chirality restraints: 1885 Sorted by residual: chirality pdb=" CA CYS D 33 " pdb=" N CYS D 33 " pdb=" C CYS D 33 " pdb=" CB CYS D 33 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA ILE D 54 " pdb=" N ILE D 54 " pdb=" C ILE D 54 " pdb=" CB ILE D 54 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA ILE C 336 " pdb=" N ILE C 336 " pdb=" C ILE C 336 " pdb=" CB ILE C 336 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 ... (remaining 1882 not shown) Planarity restraints: 3871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 243 " 0.020 2.00e-02 2.50e+03 4.03e-02 1.62e+01 pdb=" C PRO E 243 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO E 243 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG E 244 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 244 " -0.018 2.00e-02 2.50e+03 2.32e-02 1.61e+01 pdb=" CG PHE C 244 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE C 244 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 244 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE C 244 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 244 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 244 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE C 244 " 0.062 2.00e-02 2.50e+03 pdb=" HD2 PHE C 244 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE C 244 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE C 244 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE C 244 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 352 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ASN E 352 " 0.056 2.00e-02 2.50e+03 pdb=" O ASN E 352 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY E 353 " -0.019 2.00e-02 2.50e+03 ... (remaining 3868 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.99: 297 1.99 - 2.64: 29698 2.64 - 3.29: 67588 3.29 - 3.95: 89152 3.95 - 4.60: 139687 Nonbonded interactions: 326422 Sorted by model distance: nonbonded pdb=" OD1 ASP D 35 " pdb=" H HIS E 245 " model vdw 1.334 1.850 nonbonded pdb=" HZ2 TRP D 39 " pdb=" H LEU E 268 " model vdw 1.478 2.100 nonbonded pdb=" O ASN E 289 " pdb=" HG SER E 306 " model vdw 1.506 1.850 nonbonded pdb="HD22 ASN E 290 " pdb=" HE2 PHE E 304 " model vdw 1.527 2.100 nonbonded pdb="HD22 ASN A 198 " pdb=" OE2 GLU D 216 " model vdw 1.569 1.850 ... (remaining 326417 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 243 or (resid 244 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1 or name HE2 or name HZ )) or (resid 245 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or \ name HG21 or name HG22 or name HG23)) or (resid 246 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name \ HB2 or name HB3 or name HD21 or name HD22)) or resid 247 through 340)) selection = (chain 'B' and (resid 1 through 243 or (resid 244 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1 or name HE2 or name HZ )) or (resid 245 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2 or name HA or name HB or name HG1 or \ name HG21 or name HG22 or name HG23)) or (resid 246 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name \ HB2 or name HB3 or name HD21 or name HD22)) or resid 247 through 340)) selection = chain 'C' } 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=0.20 max=1.00 mean=0.99 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: 1.430 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: 0.390 Extract box with map and model: 5.740 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 80.690 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 13235 Z= 0.220 Angle : 0.646 10.092 17973 Z= 0.373 Chirality : 0.044 0.214 1885 Planarity : 0.005 0.060 2429 Dihedral : 13.581 89.045 4690 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Rotamer: Outliers : 0.98 % Allowed : 3.23 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.19), residues: 1699 helix: -1.50 (0.44), residues: 96 sheet: -0.66 (0.18), residues: 743 loop : -1.49 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 56 HIS 0.007 0.002 HIS A 21 PHE 0.021 0.002 PHE E 219 TYR 0.011 0.001 TYR E 116 ARG 0.004 0.001 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 415 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 404 time to evaluate : 1.782 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: 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 6 LYS cc_start: 0.7817 (ttpp) cc_final: 0.7512 (ttmm) REVERT: A 16 LYS cc_start: 0.8712 (pttt) cc_final: 0.8460 (pttt) REVERT: A 46 LYS cc_start: 0.8391 (mtmt) cc_final: 0.8135 (ttmm) REVERT: A 62 GLU cc_start: 0.7117 (tt0) cc_final: 0.6735 (tt0) REVERT: A 74 ASP cc_start: 0.8077 (p0) cc_final: 0.7393 (p0) REVERT: A 79 ASN cc_start: 0.7482 (m-40) cc_final: 0.7188 (m110) REVERT: A 104 VAL cc_start: 0.7626 (m) cc_final: 0.7058 (m) REVERT: A 144 PHE cc_start: 0.8299 (t80) cc_final: 0.8037 (t80) REVERT: A 178 ILE cc_start: 0.8349 (mp) cc_final: 0.8148 (mt) REVERT: A 219 LYS cc_start: 0.7897 (pttt) cc_final: 0.7697 (pttp) REVERT: A 258 LEU cc_start: 0.8744 (mm) cc_final: 0.8521 (mt) REVERT: A 267 PHE cc_start: 0.8112 (p90) cc_final: 0.7898 (p90) REVERT: A 272 SER cc_start: 0.8009 (p) cc_final: 0.7449 (t) REVERT: A 330 ASP cc_start: 0.6361 (m-30) cc_final: 0.6150 (m-30) REVERT: B 2 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6387 (tm-30) REVERT: B 6 LYS cc_start: 0.7669 (ttpp) cc_final: 0.7467 (ttmm) REVERT: B 12 ASP cc_start: 0.6566 (t0) cc_final: 0.6350 (t0) REVERT: B 16 LYS cc_start: 0.7667 (pttt) cc_final: 0.7402 (ptmm) REVERT: B 66 GLN cc_start: 0.8091 (mm110) cc_final: 0.7842 (mm-40) REVERT: B 71 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6717 (mt-10) REVERT: B 104 VAL cc_start: 0.7931 (m) cc_final: 0.7201 (m) REVERT: B 107 ASP cc_start: 0.6506 (m-30) cc_final: 0.6215 (m-30) REVERT: B 113 ASP cc_start: 0.6875 (t0) cc_final: 0.6637 (t0) REVERT: B 125 SER cc_start: 0.8068 (p) cc_final: 0.7821 (p) REVERT: B 178 ILE cc_start: 0.8589 (mp) cc_final: 0.8363 (tt) REVERT: B 181 GLU cc_start: 0.7003 (tm-30) cc_final: 0.6770 (tm-30) REVERT: B 196 ARG cc_start: 0.7525 (mtp-110) cc_final: 0.7169 (mtp85) REVERT: B 210 LYS cc_start: 0.7603 (mmmt) cc_final: 0.7399 (mmmm) REVERT: B 294 TYR cc_start: 0.7620 (p90) cc_final: 0.7390 (p90) REVERT: B 320 SER cc_start: 0.8431 (p) cc_final: 0.8141 (p) REVERT: B 321 ASP cc_start: 0.7769 (p0) cc_final: 0.6609 (p0) REVERT: C 10 LYS cc_start: 0.8232 (ttmt) cc_final: 0.8012 (ttmt) REVERT: C 14 TYR cc_start: 0.7630 (p90) cc_final: 0.7384 (p90) REVERT: C 40 TYR cc_start: 0.8450 (p90) cc_final: 0.8073 (p90) REVERT: C 58 TYR cc_start: 0.8205 (p90) cc_final: 0.7971 (p90) REVERT: C 61 TRP cc_start: 0.7742 (t60) cc_final: 0.7511 (t60) REVERT: C 104 VAL cc_start: 0.7869 (m) cc_final: 0.7363 (m) REVERT: C 158 LEU cc_start: 0.8178 (tp) cc_final: 0.7796 (tt) REVERT: C 178 ILE cc_start: 0.8294 (mp) cc_final: 0.7893 (pt) REVERT: C 185 PHE cc_start: 0.7887 (m-80) cc_final: 0.7253 (m-80) REVERT: C 253 LYS cc_start: 0.7659 (ttpt) cc_final: 0.7209 (ttmm) REVERT: C 256 ASP cc_start: 0.6755 (m-30) cc_final: 0.6335 (m-30) REVERT: C 258 LEU cc_start: 0.7993 (mm) cc_final: 0.7715 (mp) REVERT: C 282 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: C 293 ASN cc_start: 0.7383 (t0) cc_final: 0.7130 (t0) REVERT: C 323 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7770 (mmmm) REVERT: C 337 VAL cc_start: 0.8527 (t) cc_final: 0.8144 (m) REVERT: D 205 MET cc_start: -0.1603 (mtm) cc_final: -0.4260 (tpt) outliers start: 11 outliers final: 4 residues processed: 414 average time/residue: 0.5609 time to fit residues: 323.6430 Evaluate side-chains 367 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 362 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 40.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 317 GLN ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13235 Z= 0.447 Angle : 0.665 6.578 17973 Z= 0.369 Chirality : 0.047 0.154 1885 Planarity : 0.005 0.049 2429 Dihedral : 5.138 43.726 1891 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 2.71 % Allowed : 10.60 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.19), residues: 1699 helix: -0.34 (0.46), residues: 108 sheet: -0.44 (0.18), residues: 741 loop : -0.99 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 214 HIS 0.010 0.002 HIS B 21 PHE 0.017 0.002 PHE C 96 TYR 0.024 0.002 TYR E 134 ARG 0.009 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 392 time to evaluate : 1.831 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7749 (ttmm) REVERT: A 16 LYS cc_start: 0.8702 (pttt) cc_final: 0.8256 (ptpp) REVERT: A 42 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8216 (mtt180) REVERT: A 46 LYS cc_start: 0.8590 (mtmt) cc_final: 0.8162 (ttmm) REVERT: A 74 ASP cc_start: 0.8420 (p0) cc_final: 0.7830 (p0) REVERT: A 79 ASN cc_start: 0.7917 (m-40) cc_final: 0.7689 (m-40) REVERT: A 127 ASP cc_start: 0.7721 (t0) cc_final: 0.7401 (t70) REVERT: A 178 ILE cc_start: 0.8436 (mp) cc_final: 0.8218 (mt) REVERT: A 219 LYS cc_start: 0.8359 (pttt) cc_final: 0.8086 (pttp) REVERT: A 221 ASP cc_start: 0.7565 (t0) cc_final: 0.7315 (p0) REVERT: A 255 GLN cc_start: 0.7325 (mt0) cc_final: 0.6912 (mt0) REVERT: A 262 GLN cc_start: 0.7634 (mt0) cc_final: 0.7323 (mt0) REVERT: A 273 ILE cc_start: 0.8453 (mt) cc_final: 0.7941 (tp) REVERT: A 293 ASN cc_start: 0.7959 (t0) cc_final: 0.7440 (p0) REVERT: A 296 GLU cc_start: 0.7354 (tm-30) cc_final: 0.6878 (tm-30) REVERT: B 2 GLU cc_start: 0.6696 (tm-30) cc_final: 0.6492 (tm-30) REVERT: B 6 LYS cc_start: 0.8265 (ttpp) cc_final: 0.8044 (ttmm) REVERT: B 55 LEU cc_start: 0.7441 (tt) cc_final: 0.7112 (tt) REVERT: B 104 VAL cc_start: 0.7746 (m) cc_final: 0.7510 (m) REVERT: B 113 ASP cc_start: 0.7087 (t0) cc_final: 0.6877 (t0) REVERT: B 156 GLN cc_start: 0.7895 (tt0) cc_final: 0.7622 (tt0) REVERT: B 196 ARG cc_start: 0.7414 (mtp-110) cc_final: 0.7171 (mtp85) REVERT: B 207 ASN cc_start: 0.7699 (m-40) cc_final: 0.7112 (m-40) REVERT: B 210 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7825 (mmmm) REVERT: B 286 ILE cc_start: 0.8156 (mm) cc_final: 0.7867 (mt) REVERT: B 296 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7483 (tm-30) REVERT: B 321 ASP cc_start: 0.8350 (p0) cc_final: 0.6937 (p0) REVERT: B 323 LYS cc_start: 0.8460 (mmtp) cc_final: 0.8258 (mmtp) REVERT: C 6 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7542 (mtpp) REVERT: C 25 LYS cc_start: 0.7736 (mmtt) cc_final: 0.7350 (mmtt) REVERT: C 58 TYR cc_start: 0.8452 (p90) cc_final: 0.8222 (p90) REVERT: C 115 LEU cc_start: 0.7996 (mm) cc_final: 0.7741 (mt) REVERT: C 126 ASP cc_start: 0.7903 (m-30) cc_final: 0.7671 (m-30) REVERT: C 141 ASN cc_start: 0.7579 (t0) cc_final: 0.7320 (t0) REVERT: C 178 ILE cc_start: 0.8357 (mp) cc_final: 0.7942 (pt) REVERT: C 227 LEU cc_start: 0.8702 (mm) cc_final: 0.8445 (mt) REVERT: C 246 ASN cc_start: 0.8269 (t0) cc_final: 0.7953 (t0) REVERT: C 253 LYS cc_start: 0.7865 (ttpt) cc_final: 0.7312 (ttmm) REVERT: C 296 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6511 (tm-30) REVERT: C 323 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8031 (mmmm) REVERT: D 205 MET cc_start: -0.1416 (mtm) cc_final: -0.4177 (tpt) outliers start: 34 outliers final: 25 residues processed: 399 average time/residue: 0.5828 time to fit residues: 325.8774 Evaluate side-chains 387 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 362 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 153 optimal weight: 40.0000 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 40.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 198 ASN B 101 ASN B 317 GLN C 66 GLN C 76 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13235 Z= 0.286 Angle : 0.574 10.437 17973 Z= 0.315 Chirality : 0.044 0.164 1885 Planarity : 0.004 0.042 2429 Dihedral : 4.764 43.062 1886 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.38 % Allowed : 12.86 % Favored : 83.76 % 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: -0.85 (0.20), residues: 1699 helix: 0.38 (0.48), residues: 113 sheet: -0.30 (0.17), residues: 763 loop : -0.86 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 214 HIS 0.006 0.001 HIS B 21 PHE 0.014 0.001 PHE B 129 TYR 0.017 0.002 TYR C 106 ARG 0.004 0.001 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 376 time to evaluate : 1.683 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: 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 6 LYS cc_start: 0.8229 (ttpp) cc_final: 0.7807 (ttpp) REVERT: A 16 LYS cc_start: 0.8693 (pttt) cc_final: 0.8435 (ptpt) REVERT: A 42 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8368 (mtt180) REVERT: A 46 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8126 (ttmm) REVERT: A 74 ASP cc_start: 0.8266 (p0) cc_final: 0.7846 (p0) REVERT: A 79 ASN cc_start: 0.7907 (m-40) cc_final: 0.7696 (m110) REVERT: A 83 LEU cc_start: 0.8157 (mt) cc_final: 0.7928 (mp) REVERT: A 178 ILE cc_start: 0.8422 (mp) cc_final: 0.8203 (mt) REVERT: A 219 LYS cc_start: 0.8410 (pttt) cc_final: 0.8003 (pttp) REVERT: A 262 GLN cc_start: 0.7521 (mt0) cc_final: 0.7204 (mt0) REVERT: A 273 ILE cc_start: 0.8440 (mt) cc_final: 0.8075 (mt) REVERT: A 277 LYS cc_start: 0.7836 (tttt) cc_final: 0.7606 (tttt) REVERT: A 293 ASN cc_start: 0.8054 (t0) cc_final: 0.7356 (p0) REVERT: A 296 GLU cc_start: 0.7272 (tm-30) cc_final: 0.7031 (tm-30) REVERT: A 318 ILE cc_start: 0.8795 (mm) cc_final: 0.8484 (mm) REVERT: B 2 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6517 (tm-30) REVERT: B 6 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8037 (ttmm) REVERT: B 113 ASP cc_start: 0.7059 (t0) cc_final: 0.6841 (t0) REVERT: B 286 ILE cc_start: 0.8253 (mm) cc_final: 0.8008 (mt) REVERT: B 321 ASP cc_start: 0.8286 (p0) cc_final: 0.7859 (p0) REVERT: B 323 LYS cc_start: 0.8427 (mmtp) cc_final: 0.8179 (mmtp) REVERT: C 6 LYS cc_start: 0.7805 (mtpt) cc_final: 0.7556 (mtpp) REVERT: C 25 LYS cc_start: 0.7725 (mmtt) cc_final: 0.7367 (mmtt) REVERT: C 115 LEU cc_start: 0.8020 (mm) cc_final: 0.7687 (mt) REVERT: C 227 LEU cc_start: 0.8680 (mm) cc_final: 0.8421 (mt) REVERT: C 246 ASN cc_start: 0.8273 (t0) cc_final: 0.8026 (t0) REVERT: C 253 LYS cc_start: 0.7770 (ttpt) cc_final: 0.7147 (ttmm) REVERT: C 254 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7560 (p) REVERT: C 296 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6471 (tm-30) REVERT: C 305 LYS cc_start: 0.8614 (ptpt) cc_final: 0.8319 (ptpp) REVERT: C 323 LYS cc_start: 0.8291 (mmtt) cc_final: 0.8069 (mmmm) REVERT: C 330 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7672 (p0) REVERT: D 205 MET cc_start: -0.1249 (mtm) cc_final: -0.4147 (tpt) outliers start: 42 outliers final: 32 residues processed: 390 average time/residue: 0.5690 time to fit residues: 309.5805 Evaluate side-chains 399 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 365 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 317 GLN Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 103 optimal weight: 6.9990 chunk 154 optimal weight: 50.0000 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN B 60 GLN B 264 GLN B 317 GLN ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 13235 Z= 0.440 Angle : 0.613 7.546 17973 Z= 0.342 Chirality : 0.046 0.175 1885 Planarity : 0.004 0.078 2429 Dihedral : 4.826 42.743 1885 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.03 % Favored : 95.91 % Rotamer: Outliers : 3.91 % Allowed : 14.44 % Favored : 81.65 % 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: -0.98 (0.20), residues: 1699 helix: 0.42 (0.49), residues: 116 sheet: -0.38 (0.17), residues: 762 loop : -0.98 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 214 HIS 0.009 0.001 HIS B 21 PHE 0.019 0.002 PHE B 129 TYR 0.019 0.002 TYR C 226 ARG 0.011 0.001 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 418 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 369 time to evaluate : 1.620 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: 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: symmetry clash revert: symmetry clash REVERT: A 6 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7911 (ttpp) REVERT: A 7 ASP cc_start: 0.7578 (t70) cc_final: 0.7165 (t70) REVERT: A 16 LYS cc_start: 0.8759 (pttt) cc_final: 0.8556 (ptmt) REVERT: A 46 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8093 (ttmm) REVERT: A 74 ASP cc_start: 0.8372 (p0) cc_final: 0.7957 (p0) REVERT: A 178 ILE cc_start: 0.8441 (mp) cc_final: 0.8207 (mt) REVERT: A 219 LYS cc_start: 0.8433 (pttt) cc_final: 0.8145 (pttp) REVERT: A 260 VAL cc_start: 0.8293 (t) cc_final: 0.7842 (m) REVERT: A 262 GLN cc_start: 0.7523 (mt0) cc_final: 0.7287 (mt0) REVERT: A 273 ILE cc_start: 0.8475 (mt) cc_final: 0.8074 (mt) REVERT: A 277 LYS cc_start: 0.7870 (tttt) cc_final: 0.7618 (tttt) REVERT: A 293 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7628 (p0) REVERT: B 98 TYR cc_start: 0.7760 (t80) cc_final: 0.7272 (t80) REVERT: B 113 ASP cc_start: 0.7082 (t0) cc_final: 0.6827 (t0) REVERT: B 207 ASN cc_start: 0.7820 (m-40) cc_final: 0.7600 (m-40) REVERT: B 264 GLN cc_start: 0.8582 (tp40) cc_final: 0.8360 (tp-100) REVERT: B 286 ILE cc_start: 0.8312 (mm) cc_final: 0.8032 (mt) REVERT: B 323 LYS cc_start: 0.8484 (mmtp) cc_final: 0.8234 (mmtp) REVERT: C 2 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6336 (tm-30) REVERT: C 6 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7682 (mtpp) REVERT: C 25 LYS cc_start: 0.7761 (mmtt) cc_final: 0.7408 (mmtt) REVERT: C 115 LEU cc_start: 0.8220 (mm) cc_final: 0.7952 (mt) REVERT: C 181 GLU cc_start: 0.6648 (tm-30) cc_final: 0.6446 (tm-30) REVERT: C 227 LEU cc_start: 0.8681 (mm) cc_final: 0.8440 (mt) REVERT: C 246 ASN cc_start: 0.8320 (t0) cc_final: 0.7979 (t0) REVERT: C 253 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7375 (ttmm) REVERT: C 296 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6546 (tm-30) REVERT: C 323 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8136 (mmmm) REVERT: C 330 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7638 (p0) REVERT: D 205 MET cc_start: -0.1036 (mtm) cc_final: -0.3929 (tpt) outliers start: 49 outliers final: 41 residues processed: 388 average time/residue: 0.5556 time to fit residues: 302.2479 Evaluate side-chains 408 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 365 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 255 GLN Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13235 Z= 0.339 Angle : 0.572 5.038 17973 Z= 0.318 Chirality : 0.044 0.167 1885 Planarity : 0.004 0.039 2429 Dihedral : 4.737 42.654 1885 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.91 % Allowed : 16.47 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.20), residues: 1699 helix: 0.72 (0.50), residues: 116 sheet: -0.35 (0.17), residues: 760 loop : -1.06 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 214 HIS 0.007 0.001 HIS B 21 PHE 0.018 0.002 PHE B 129 TYR 0.016 0.002 TYR B 58 ARG 0.006 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 373 time to evaluate : 1.814 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: 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: symmetry clash REVERT: A 7 ASP cc_start: 0.7593 (t70) cc_final: 0.7101 (t70) REVERT: A 16 LYS cc_start: 0.8764 (pttt) cc_final: 0.8555 (ptmt) REVERT: A 46 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8089 (ttmm) REVERT: A 83 LEU cc_start: 0.8177 (mt) cc_final: 0.7968 (mp) REVERT: A 210 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8387 (mmmt) REVERT: A 218 LEU cc_start: 0.8456 (tp) cc_final: 0.8166 (mm) REVERT: A 219 LYS cc_start: 0.8446 (pttt) cc_final: 0.8138 (pttp) REVERT: A 260 VAL cc_start: 0.8301 (t) cc_final: 0.7850 (m) REVERT: A 273 ILE cc_start: 0.8341 (mt) cc_final: 0.8048 (mt) REVERT: A 277 LYS cc_start: 0.7852 (tttt) cc_final: 0.7598 (tttt) REVERT: A 293 ASN cc_start: 0.8301 (OUTLIER) cc_final: 0.7566 (p0) REVERT: A 328 SER cc_start: 0.8233 (m) cc_final: 0.8019 (p) REVERT: B 98 TYR cc_start: 0.7753 (t80) cc_final: 0.7360 (t80) REVERT: B 168 ARG cc_start: 0.8702 (mmt90) cc_final: 0.8367 (mmt180) REVERT: B 264 GLN cc_start: 0.8534 (tp40) cc_final: 0.8292 (tp-100) REVERT: B 286 ILE cc_start: 0.8281 (mm) cc_final: 0.8010 (mt) REVERT: B 323 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8236 (mmtp) REVERT: C 6 LYS cc_start: 0.7932 (mtpt) cc_final: 0.7693 (mtpp) REVERT: C 25 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7428 (mmtt) REVERT: C 97 ASP cc_start: 0.6902 (p0) cc_final: 0.6438 (p0) REVERT: C 115 LEU cc_start: 0.8298 (mm) cc_final: 0.8037 (mt) REVERT: C 138 THR cc_start: 0.8201 (m) cc_final: 0.7700 (p) REVERT: C 227 LEU cc_start: 0.8665 (mm) cc_final: 0.8423 (mt) REVERT: C 246 ASN cc_start: 0.8316 (t0) cc_final: 0.7987 (t0) REVERT: C 296 GLU cc_start: 0.7234 (tm-30) cc_final: 0.6571 (tm-30) REVERT: C 323 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8103 (mmmm) REVERT: C 330 ASP cc_start: 0.8067 (p0) cc_final: 0.7746 (p0) REVERT: D 205 MET cc_start: -0.1010 (mtm) cc_final: -0.3939 (tpt) outliers start: 49 outliers final: 39 residues processed: 394 average time/residue: 0.6000 time to fit residues: 330.6713 Evaluate side-chains 406 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 366 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 317 GLN C 200 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 13235 Z= 0.374 Angle : 0.587 5.316 17973 Z= 0.325 Chirality : 0.045 0.200 1885 Planarity : 0.004 0.071 2429 Dihedral : 4.718 42.678 1885 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.36 % Allowed : 16.92 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.20), residues: 1699 helix: 0.91 (0.50), residues: 119 sheet: -0.37 (0.17), residues: 760 loop : -1.16 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 214 HIS 0.007 0.001 HIS B 21 PHE 0.027 0.002 PHE B 118 TYR 0.019 0.002 TYR B 58 ARG 0.007 0.001 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 379 time to evaluate : 1.940 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 7 ASP cc_start: 0.7636 (t70) cc_final: 0.7063 (t70) REVERT: A 16 LYS cc_start: 0.8723 (pttt) cc_final: 0.8457 (ptpt) REVERT: A 20 LEU cc_start: 0.8419 (tp) cc_final: 0.8118 (tp) REVERT: A 46 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8106 (ttmm) REVERT: A 210 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8420 (mmmt) REVERT: A 219 LYS cc_start: 0.8450 (pttt) cc_final: 0.8137 (pttp) REVERT: A 255 GLN cc_start: 0.7135 (mt0) cc_final: 0.6711 (mt0) REVERT: A 260 VAL cc_start: 0.8299 (t) cc_final: 0.7901 (m) REVERT: A 273 ILE cc_start: 0.8319 (mt) cc_final: 0.8088 (mt) REVERT: A 277 LYS cc_start: 0.7905 (tttt) cc_final: 0.7684 (tttt) REVERT: A 328 SER cc_start: 0.8344 (m) cc_final: 0.8106 (p) REVERT: B 16 LYS cc_start: 0.8138 (ptmt) cc_final: 0.7847 (ptmt) REVERT: B 54 ASP cc_start: 0.6480 (p0) cc_final: 0.6193 (p0) REVERT: B 98 TYR cc_start: 0.7817 (t80) cc_final: 0.7456 (t80) REVERT: B 113 ASP cc_start: 0.7126 (t0) cc_final: 0.6867 (t0) REVERT: B 264 GLN cc_start: 0.8548 (tp40) cc_final: 0.8160 (tp-100) REVERT: B 286 ILE cc_start: 0.8263 (mm) cc_final: 0.7990 (mt) REVERT: B 323 LYS cc_start: 0.8521 (mmtp) cc_final: 0.8231 (mmtp) REVERT: C 6 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7734 (mtpp) REVERT: C 16 LYS cc_start: 0.8662 (pttt) cc_final: 0.8268 (ptpp) REVERT: C 25 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7388 (mmtt) REVERT: C 46 LYS cc_start: 0.8547 (mtmm) cc_final: 0.8336 (mtmm) REVERT: C 97 ASP cc_start: 0.6833 (p0) cc_final: 0.6473 (p0) REVERT: C 112 THR cc_start: 0.8218 (p) cc_final: 0.7872 (t) REVERT: C 115 LEU cc_start: 0.8299 (mm) cc_final: 0.8052 (mt) REVERT: C 138 THR cc_start: 0.8180 (m) cc_final: 0.7719 (p) REVERT: C 227 LEU cc_start: 0.8640 (mm) cc_final: 0.8420 (mt) REVERT: C 238 THR cc_start: 0.9235 (m) cc_final: 0.8985 (p) REVERT: C 246 ASN cc_start: 0.8335 (t0) cc_final: 0.8022 (t0) REVERT: C 253 LYS cc_start: 0.7897 (ttpt) cc_final: 0.7527 (mtpp) REVERT: C 296 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6608 (tm-30) REVERT: C 323 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8118 (mmmm) REVERT: C 337 VAL cc_start: 0.8384 (t) cc_final: 0.8054 (p) REVERT: D 205 MET cc_start: -0.0922 (mtm) cc_final: -0.3915 (tpt) outliers start: 55 outliers final: 49 residues processed: 403 average time/residue: 0.5545 time to fit residues: 308.1711 Evaluate side-chains 420 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 371 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 201 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 310 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 305 LYS Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 162 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN B 60 GLN B 200 GLN C 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13235 Z= 0.185 Angle : 0.529 5.124 17973 Z= 0.291 Chirality : 0.044 0.193 1885 Planarity : 0.003 0.045 2429 Dihedral : 4.483 41.563 1885 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.93 % Allowed : 18.27 % Favored : 78.80 % 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: -0.76 (0.20), residues: 1699 helix: 1.16 (0.51), residues: 119 sheet: -0.19 (0.18), residues: 763 loop : -1.00 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 39 HIS 0.005 0.001 HIS C 21 PHE 0.016 0.001 PHE B 118 TYR 0.012 0.001 TYR A 338 ARG 0.005 0.000 ARG B 140 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 416 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 380 time to evaluate : 1.735 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7163 (tm-30) REVERT: A 7 ASP cc_start: 0.7532 (t70) cc_final: 0.6956 (t70) REVERT: A 16 LYS cc_start: 0.8700 (pttt) cc_final: 0.8430 (ptpt) REVERT: A 20 LEU cc_start: 0.8441 (tp) cc_final: 0.8091 (tp) REVERT: A 42 ARG cc_start: 0.8518 (mtt180) cc_final: 0.8236 (mtt180) REVERT: A 46 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8042 (ttmm) REVERT: A 83 LEU cc_start: 0.8168 (mt) cc_final: 0.7943 (mp) REVERT: A 177 SER cc_start: 0.8263 (t) cc_final: 0.7946 (p) REVERT: A 218 LEU cc_start: 0.8413 (tp) cc_final: 0.8117 (mm) REVERT: A 219 LYS cc_start: 0.8422 (pttt) cc_final: 0.8068 (pttp) REVERT: A 260 VAL cc_start: 0.8282 (t) cc_final: 0.7873 (m) REVERT: A 277 LYS cc_start: 0.7887 (tttt) cc_final: 0.7607 (tttt) REVERT: A 328 SER cc_start: 0.8312 (m) cc_final: 0.8079 (p) REVERT: B 16 LYS cc_start: 0.8110 (ptmt) cc_final: 0.7811 (ptmt) REVERT: B 54 ASP cc_start: 0.6438 (p0) cc_final: 0.6163 (p0) REVERT: B 98 TYR cc_start: 0.7652 (t80) cc_final: 0.7263 (t80) REVERT: B 125 SER cc_start: 0.8451 (m) cc_final: 0.7926 (t) REVERT: B 264 GLN cc_start: 0.8453 (tp40) cc_final: 0.8065 (tp-100) REVERT: B 286 ILE cc_start: 0.8269 (mm) cc_final: 0.7995 (mt) REVERT: C 6 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7736 (mtpp) REVERT: C 16 LYS cc_start: 0.8620 (pttt) cc_final: 0.8267 (ptpp) REVERT: C 25 LYS cc_start: 0.7820 (mmtt) cc_final: 0.7489 (mmtt) REVERT: C 97 ASP cc_start: 0.6635 (p0) cc_final: 0.6344 (p0) REVERT: C 112 THR cc_start: 0.8172 (p) cc_final: 0.7855 (t) REVERT: C 115 LEU cc_start: 0.8310 (mm) cc_final: 0.8061 (mt) REVERT: C 138 THR cc_start: 0.8165 (m) cc_final: 0.7713 (p) REVERT: C 227 LEU cc_start: 0.8584 (mm) cc_final: 0.8354 (mt) REVERT: C 238 THR cc_start: 0.9183 (m) cc_final: 0.8914 (p) REVERT: C 246 ASN cc_start: 0.8305 (t0) cc_final: 0.8002 (t0) REVERT: C 253 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7449 (mtpp) REVERT: C 296 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6589 (tm-30) REVERT: C 323 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8092 (mmmm) REVERT: C 330 ASP cc_start: 0.8122 (p0) cc_final: 0.7845 (p0) REVERT: C 337 VAL cc_start: 0.8389 (t) cc_final: 0.8083 (p) REVERT: D 205 MET cc_start: -0.0860 (mtm) cc_final: -0.3883 (tpt) outliers start: 36 outliers final: 30 residues processed: 394 average time/residue: 0.6078 time to fit residues: 332.0462 Evaluate side-chains 407 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 377 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 148 optimal weight: 30.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13235 Z= 0.258 Angle : 0.540 5.297 17973 Z= 0.297 Chirality : 0.043 0.182 1885 Planarity : 0.004 0.043 2429 Dihedral : 4.444 40.799 1885 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.46 % Allowed : 17.67 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.20), residues: 1699 helix: 1.16 (0.51), residues: 119 sheet: -0.20 (0.18), residues: 763 loop : -1.05 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 214 HIS 0.004 0.001 HIS B 21 PHE 0.014 0.001 PHE B 129 TYR 0.015 0.002 TYR A 58 ARG 0.012 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 424 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 381 time to evaluate : 1.871 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASP cc_start: 0.7555 (t70) cc_final: 0.6957 (t70) REVERT: A 16 LYS cc_start: 0.8711 (pttt) cc_final: 0.8437 (ptpt) REVERT: A 20 LEU cc_start: 0.8465 (tp) cc_final: 0.8166 (tp) REVERT: A 42 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8209 (mtt180) REVERT: A 46 LYS cc_start: 0.8477 (mtmt) cc_final: 0.8037 (ttmm) REVERT: A 83 LEU cc_start: 0.8190 (mt) cc_final: 0.7958 (mp) REVERT: A 177 SER cc_start: 0.8246 (t) cc_final: 0.7899 (p) REVERT: A 219 LYS cc_start: 0.8426 (pttt) cc_final: 0.8118 (pttp) REVERT: A 260 VAL cc_start: 0.8302 (t) cc_final: 0.7890 (m) REVERT: A 277 LYS cc_start: 0.7879 (tttt) cc_final: 0.7607 (tttt) REVERT: A 292 VAL cc_start: 0.8761 (m) cc_final: 0.8276 (p) REVERT: A 328 SER cc_start: 0.8338 (m) cc_final: 0.8111 (p) REVERT: B 16 LYS cc_start: 0.8116 (ptmt) cc_final: 0.7765 (ptmt) REVERT: B 54 ASP cc_start: 0.6412 (p0) cc_final: 0.6084 (p0) REVERT: B 98 TYR cc_start: 0.7692 (t80) cc_final: 0.7327 (t80) REVERT: B 107 ASP cc_start: 0.6837 (m-30) cc_final: 0.6624 (m-30) REVERT: B 113 ASP cc_start: 0.7095 (t0) cc_final: 0.6861 (t0) REVERT: B 125 SER cc_start: 0.8457 (m) cc_final: 0.7920 (t) REVERT: B 136 VAL cc_start: 0.9128 (m) cc_final: 0.8668 (p) REVERT: B 264 GLN cc_start: 0.8485 (tp40) cc_final: 0.8023 (tp-100) REVERT: B 286 ILE cc_start: 0.8276 (mm) cc_final: 0.8005 (mt) REVERT: B 323 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8195 (mmtp) REVERT: C 6 LYS cc_start: 0.7853 (mtpt) cc_final: 0.7582 (mtpp) REVERT: C 16 LYS cc_start: 0.8630 (pttt) cc_final: 0.8264 (ptpp) REVERT: C 25 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7502 (mmtt) REVERT: C 106 TYR cc_start: 0.8234 (t80) cc_final: 0.8026 (t80) REVERT: C 112 THR cc_start: 0.8198 (p) cc_final: 0.7874 (t) REVERT: C 113 ASP cc_start: 0.7438 (t0) cc_final: 0.7201 (t0) REVERT: C 115 LEU cc_start: 0.8358 (mm) cc_final: 0.8112 (mt) REVERT: C 138 THR cc_start: 0.8193 (m) cc_final: 0.7609 (p) REVERT: C 227 LEU cc_start: 0.8567 (mm) cc_final: 0.8359 (mt) REVERT: C 238 THR cc_start: 0.9207 (m) cc_final: 0.8923 (p) REVERT: C 246 ASN cc_start: 0.8283 (t0) cc_final: 0.7990 (t0) REVERT: C 253 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7448 (mtpp) REVERT: C 296 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6638 (tm-30) REVERT: C 323 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8094 (mmmm) REVERT: C 330 ASP cc_start: 0.8173 (p0) cc_final: 0.7875 (p0) REVERT: C 337 VAL cc_start: 0.8397 (t) cc_final: 0.8092 (p) REVERT: D 205 MET cc_start: -0.0795 (mtm) cc_final: -0.3854 (tpt) outliers start: 43 outliers final: 43 residues processed: 399 average time/residue: 0.5735 time to fit residues: 316.7627 Evaluate side-chains 422 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 379 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 0.8980 chunk 142 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 160 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13235 Z= 0.216 Angle : 0.531 5.741 17973 Z= 0.291 Chirality : 0.043 0.194 1885 Planarity : 0.003 0.039 2429 Dihedral : 4.361 40.255 1885 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.38 % Allowed : 17.67 % Favored : 78.95 % 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: -0.70 (0.20), residues: 1699 helix: 1.32 (0.51), residues: 119 sheet: -0.17 (0.18), residues: 769 loop : -0.96 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 39 HIS 0.004 0.001 HIS D 55 PHE 0.024 0.001 PHE B 118 TYR 0.019 0.001 TYR C 4 ARG 0.008 0.001 ARG C 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 423 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 381 time to evaluate : 1.865 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: 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 7 ASP cc_start: 0.7520 (t70) cc_final: 0.6930 (t70) REVERT: A 16 LYS cc_start: 0.8721 (pttt) cc_final: 0.8440 (ptpt) REVERT: A 20 LEU cc_start: 0.8429 (tp) cc_final: 0.8147 (tp) REVERT: A 42 ARG cc_start: 0.8493 (mtt180) cc_final: 0.8216 (mtt180) REVERT: A 46 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8052 (ttmm) REVERT: A 83 LEU cc_start: 0.8150 (mt) cc_final: 0.7948 (mp) REVERT: A 127 ASP cc_start: 0.7705 (t0) cc_final: 0.7345 (t70) REVERT: A 177 SER cc_start: 0.8170 (t) cc_final: 0.7802 (p) REVERT: A 219 LYS cc_start: 0.8422 (pttt) cc_final: 0.8176 (pttp) REVERT: A 221 ASP cc_start: 0.7285 (t70) cc_final: 0.6981 (p0) REVERT: A 277 LYS cc_start: 0.7862 (tttt) cc_final: 0.7601 (tttt) REVERT: A 292 VAL cc_start: 0.8761 (m) cc_final: 0.8293 (p) REVERT: B 16 LYS cc_start: 0.8100 (ptmt) cc_final: 0.7768 (ptmt) REVERT: B 54 ASP cc_start: 0.6500 (p0) cc_final: 0.6180 (p0) REVERT: B 98 TYR cc_start: 0.7672 (t80) cc_final: 0.7298 (t80) REVERT: B 107 ASP cc_start: 0.6850 (m-30) cc_final: 0.6642 (m-30) REVERT: B 125 SER cc_start: 0.8462 (m) cc_final: 0.7940 (t) REVERT: B 136 VAL cc_start: 0.9156 (m) cc_final: 0.8682 (p) REVERT: B 264 GLN cc_start: 0.8494 (tp40) cc_final: 0.8039 (tp-100) REVERT: B 273 ILE cc_start: 0.8093 (mt) cc_final: 0.7846 (tt) REVERT: B 286 ILE cc_start: 0.8276 (mm) cc_final: 0.7992 (mt) REVERT: C 6 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7627 (mtpp) REVERT: C 16 LYS cc_start: 0.8647 (pttt) cc_final: 0.8277 (ptpp) REVERT: C 25 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7518 (mmtt) REVERT: C 106 TYR cc_start: 0.8193 (t80) cc_final: 0.7979 (t80) REVERT: C 112 THR cc_start: 0.8175 (p) cc_final: 0.7868 (t) REVERT: C 113 ASP cc_start: 0.7438 (t0) cc_final: 0.7227 (t0) REVERT: C 115 LEU cc_start: 0.8295 (mm) cc_final: 0.8031 (mt) REVERT: C 138 THR cc_start: 0.8190 (m) cc_final: 0.7603 (p) REVERT: C 227 LEU cc_start: 0.8541 (mm) cc_final: 0.8333 (mt) REVERT: C 238 THR cc_start: 0.9195 (m) cc_final: 0.8934 (p) REVERT: C 246 ASN cc_start: 0.8314 (t0) cc_final: 0.8020 (t0) REVERT: C 253 LYS cc_start: 0.7909 (ttpt) cc_final: 0.7440 (mtpp) REVERT: C 296 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6697 (tm-30) REVERT: C 323 LYS cc_start: 0.8410 (mmtt) cc_final: 0.8095 (mmmm) REVERT: C 330 ASP cc_start: 0.8203 (p0) cc_final: 0.7800 (p0) REVERT: C 337 VAL cc_start: 0.8385 (t) cc_final: 0.8144 (p) REVERT: D 205 MET cc_start: -0.0742 (mtm) cc_final: -0.3838 (tpt) outliers start: 42 outliers final: 38 residues processed: 398 average time/residue: 0.5733 time to fit residues: 314.8447 Evaluate side-chains 412 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 374 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 chunk 168 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 134 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13235 Z= 0.272 Angle : 0.545 5.651 17973 Z= 0.300 Chirality : 0.043 0.184 1885 Planarity : 0.004 0.043 2429 Dihedral : 4.377 39.412 1885 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.68 % Allowed : 17.97 % Favored : 78.35 % 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: -0.73 (0.20), residues: 1699 helix: 1.35 (0.51), residues: 119 sheet: -0.19 (0.18), residues: 769 loop : -0.99 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 214 HIS 0.004 0.001 HIS C 21 PHE 0.015 0.001 PHE B 129 TYR 0.023 0.002 TYR A 14 ARG 0.006 0.001 ARG C 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 16 is missing expected H atoms. Skipping. Residue SER 17 is missing expected H atoms. Skipping. Residue THR 25 is missing expected H atoms. Skipping. Residue ILE 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue SER 30 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Residue SER 52 is missing expected H atoms. Skipping. Residue ILE 54 is missing expected H atoms. Skipping. Evaluate side-chains 424 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 378 time to evaluate : 1.746 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: 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: symmetry clash REVERT: A 7 ASP cc_start: 0.7582 (t70) cc_final: 0.6952 (t0) REVERT: A 16 LYS cc_start: 0.8760 (pttt) cc_final: 0.8448 (ptpt) REVERT: A 20 LEU cc_start: 0.8450 (tp) cc_final: 0.8205 (tp) REVERT: A 42 ARG cc_start: 0.8551 (mtt180) cc_final: 0.8207 (mtt180) REVERT: A 46 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8032 (ttmm) REVERT: A 83 LEU cc_start: 0.8157 (mt) cc_final: 0.7941 (mp) REVERT: A 127 ASP cc_start: 0.7735 (t0) cc_final: 0.7376 (t70) REVERT: A 177 SER cc_start: 0.8165 (t) cc_final: 0.7794 (p) REVERT: A 219 LYS cc_start: 0.8429 (pttt) cc_final: 0.8127 (pttp) REVERT: A 221 ASP cc_start: 0.7287 (t70) cc_final: 0.6950 (p0) REVERT: A 260 VAL cc_start: 0.8310 (t) cc_final: 0.7922 (m) REVERT: A 292 VAL cc_start: 0.8758 (m) cc_final: 0.8307 (p) REVERT: B 16 LYS cc_start: 0.8107 (ptmt) cc_final: 0.7783 (ptmt) REVERT: B 54 ASP cc_start: 0.6496 (p0) cc_final: 0.6172 (p0) REVERT: B 98 TYR cc_start: 0.7703 (t80) cc_final: 0.7337 (t80) REVERT: B 107 ASP cc_start: 0.6897 (m-30) cc_final: 0.6662 (m-30) REVERT: B 125 SER cc_start: 0.8472 (m) cc_final: 0.7944 (t) REVERT: B 136 VAL cc_start: 0.9158 (m) cc_final: 0.8678 (p) REVERT: B 273 ILE cc_start: 0.8124 (mt) cc_final: 0.7870 (tt) REVERT: B 286 ILE cc_start: 0.8273 (mm) cc_final: 0.7982 (mt) REVERT: C 6 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7627 (mtpp) REVERT: C 16 LYS cc_start: 0.8653 (pttt) cc_final: 0.8289 (ptpp) REVERT: C 25 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7508 (mmtt) REVERT: C 106 TYR cc_start: 0.8224 (t80) cc_final: 0.8019 (t80) REVERT: C 112 THR cc_start: 0.8281 (p) cc_final: 0.7949 (t) REVERT: C 113 ASP cc_start: 0.7469 (t0) cc_final: 0.7266 (t0) REVERT: C 115 LEU cc_start: 0.8264 (mm) cc_final: 0.7996 (mt) REVERT: C 138 THR cc_start: 0.8197 (m) cc_final: 0.7601 (p) REVERT: C 238 THR cc_start: 0.9193 (m) cc_final: 0.8900 (p) REVERT: C 246 ASN cc_start: 0.8282 (t0) cc_final: 0.7987 (t0) REVERT: C 253 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7449 (mtpp) REVERT: C 296 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6702 (tm-30) REVERT: C 323 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8106 (mmmm) REVERT: C 337 VAL cc_start: 0.8394 (t) cc_final: 0.8115 (p) REVERT: D 205 MET cc_start: -0.0678 (mtm) cc_final: -0.3809 (tpt) outliers start: 46 outliers final: 44 residues processed: 396 average time/residue: 0.5618 time to fit residues: 306.4711 Evaluate side-chains 422 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 378 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 TYR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 236 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 336 ILE Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 76 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 LYS Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 153 PHE Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 339 GLN Chi-restraints excluded: chain D residue 56 TRP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain E residue 134 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 0.0060 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.201300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139422 restraints weight = 105742.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144620 restraints weight = 27862.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.146687 restraints weight = 9895.070| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13235 Z= 0.169 Angle : 0.516 5.562 17973 Z= 0.282 Chirality : 0.043 0.189 1885 Planarity : 0.003 0.043 2429 Dihedral : 4.251 38.181 1885 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 19.02 % Favored : 78.12 % 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: -0.54 (0.20), residues: 1699 helix: 1.56 (0.52), residues: 119 sheet: -0.05 (0.18), residues: 769 loop : -0.89 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 39 HIS 0.004 0.001 HIS C 21 PHE 0.012 0.001 PHE A 96 TYR 0.018 0.001 TYR A 14 ARG 0.005 0.000 ARG B 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6665.64 seconds wall clock time: 118 minutes 3.79 seconds (7083.79 seconds total)