Starting phenix.real_space_refine on Sat Nov 18 15:06:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/11_2023/7nst_12576.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/11_2023/7nst_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_12576/11_2023/7nst_12576.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/11_2023/7nst_12576.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/11_2023/7nst_12576.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nst_12576/11_2023/7nst_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-1.21rc1-5144/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: 14.63, per 1000 atoms: 0.62 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: 19.86 Conformation dependent library (CDL) restraints added in 4.2 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: 1.88 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: 8.55 Time building geometry restraints manager: 20.59 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: 9116 17.81 - 35.62: 650 35.62 - 53.43: 96 53.43 - 71.24: 41 71.24 - 89.04: 9 Dihedral angle restraints: 9912 sinusoidal: 4222 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 9909 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: 0.920 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: 0.440 Extract box with map and model: 5.950 Check model and map are aligned: 0.420 Set scattering table: 0.240 Process input model: 83.040 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.030 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.828 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 outliers start: 11 outliers final: 4 residues processed: 414 average time/residue: 0.5629 time to fit residues: 323.4385 Evaluate side-chains 359 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 355 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2809 time to fit residues: 4.2855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 6.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 50.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 317 GLN C 66 GLN C 101 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 13235 Z= 0.537 Angle : 0.709 6.520 17973 Z= 0.394 Chirality : 0.049 0.166 1885 Planarity : 0.005 0.052 2429 Dihedral : 4.995 29.200 1883 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.08 % Favored : 96.86 % Rotamer: Outliers : 3.23 % Allowed : 11.95 % Favored : 84.81 % 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: -1.24 (0.19), residues: 1699 helix: -0.45 (0.46), residues: 108 sheet: -0.51 (0.18), residues: 741 loop : -1.08 (0.21), residues: 850 *********************** 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 428 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 387 time to evaluate : 1.820 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 outliers start: 41 outliers final: 31 residues processed: 401 average time/residue: 0.5868 time to fit residues: 325.3827 Evaluate side-chains 388 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 357 time to evaluate : 1.988 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3048 time to fit residues: 18.9788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 223 ASN B 101 ASN B 252 ASN B 264 GLN B 317 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 13235 Z= 0.544 Angle : 0.674 6.669 17973 Z= 0.378 Chirality : 0.048 0.223 1885 Planarity : 0.004 0.042 2429 Dihedral : 4.932 22.120 1883 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.95 % Allowed : 15.79 % Favored : 82.26 % 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: -1.28 (0.19), residues: 1699 helix: -0.26 (0.47), residues: 116 sheet: -0.53 (0.17), residues: 764 loop : -1.15 (0.21), residues: 819 *********************** 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 395 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 372 time to evaluate : 1.805 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 outliers start: 23 outliers final: 19 residues processed: 378 average time/residue: 0.6211 time to fit residues: 325.2880 Evaluate side-chains 379 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 360 time to evaluate : 1.857 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.4133 time to fit residues: 15.1672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 30.0000 chunk 163 optimal weight: 50.0000 chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN C 66 GLN C 200 GLN ** E 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13235 Z= 0.282 Angle : 0.578 5.591 17973 Z= 0.320 Chirality : 0.044 0.160 1885 Planarity : 0.004 0.051 2429 Dihedral : 4.605 19.814 1883 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.73 % Allowed : 16.32 % Favored : 81.95 % 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: -1.07 (0.19), residues: 1699 helix: 0.26 (0.47), residues: 119 sheet: -0.37 (0.17), residues: 750 loop : -1.12 (0.21), residues: 830 *********************** 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 395 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 375 time to evaluate : 1.833 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 outliers start: 20 outliers final: 15 residues processed: 385 average time/residue: 0.5946 time to fit residues: 314.0894 Evaluate side-chains 383 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 368 time to evaluate : 1.675 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3209 time to fit residues: 10.3296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN E 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13235 Z= 0.251 Angle : 0.558 5.538 17973 Z= 0.308 Chirality : 0.044 0.158 1885 Planarity : 0.004 0.062 2429 Dihedral : 4.434 19.543 1883 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.43 % Allowed : 17.07 % Favored : 81.50 % 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: -0.96 (0.19), residues: 1699 helix: 0.61 (0.49), residues: 119 sheet: -0.27 (0.18), residues: 745 loop : -1.11 (0.21), residues: 835 *********************** 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 393 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 377 time to evaluate : 1.844 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 outliers start: 16 outliers final: 10 residues processed: 379 average time/residue: 0.6168 time to fit residues: 321.0303 Evaluate side-chains 374 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 364 time to evaluate : 1.823 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.3856 time to fit residues: 8.3614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 213 GLN A 262 GLN B 69 ASN B 200 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13235 Z= 0.243 Angle : 0.551 6.024 17973 Z= 0.302 Chirality : 0.044 0.161 1885 Planarity : 0.003 0.042 2429 Dihedral : 4.331 19.454 1883 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.58 % Allowed : 18.35 % Favored : 80.08 % 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: -0.86 (0.20), residues: 1699 helix: 0.91 (0.50), residues: 119 sheet: -0.20 (0.18), residues: 745 loop : -1.08 (0.21), residues: 835 *********************** 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 390 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 372 time to evaluate : 1.873 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 outliers start: 18 outliers final: 13 residues processed: 377 average time/residue: 0.5996 time to fit residues: 309.8950 Evaluate side-chains 382 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 369 time to evaluate : 1.873 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.3735 time to fit residues: 10.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 92 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 162 optimal weight: 40.0000 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 213 GLN A 262 GLN B 252 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13235 Z= 0.186 Angle : 0.534 5.231 17973 Z= 0.293 Chirality : 0.044 0.179 1885 Planarity : 0.003 0.043 2429 Dihedral : 4.215 20.667 1883 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.20 % Allowed : 18.42 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1699 helix: 1.06 (0.51), residues: 119 sheet: -0.07 (0.18), residues: 751 loop : -1.04 (0.21), residues: 829 *********************** 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 380 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 367 time to evaluate : 1.895 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 outliers start: 13 outliers final: 8 residues processed: 371 average time/residue: 0.6446 time to fit residues: 328.3845 Evaluate side-chains 365 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 357 time to evaluate : 1.816 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 8 average time/residue: 0.3162 time to fit residues: 6.7897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 262 GLN D 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 13235 Z= 0.435 Angle : 0.617 5.997 17973 Z= 0.343 Chirality : 0.045 0.188 1885 Planarity : 0.004 0.041 2429 Dihedral : 4.481 20.250 1883 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 2.03 % Allowed : 19.10 % 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: -1.06 (0.20), residues: 1699 helix: 0.88 (0.50), residues: 119 sheet: -0.39 (0.17), residues: 772 loop : -1.19 (0.21), residues: 808 *********************** 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 383 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 359 time to evaluate : 1.929 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 outliers start: 24 outliers final: 19 residues processed: 365 average time/residue: 0.6389 time to fit residues: 319.5995 Evaluate side-chains 374 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 355 time to evaluate : 2.080 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.3801 time to fit residues: 13.7340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13235 Z= 0.366 Angle : 0.597 6.341 17973 Z= 0.330 Chirality : 0.045 0.180 1885 Planarity : 0.004 0.083 2429 Dihedral : 4.468 20.378 1883 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.28 % Allowed : 18.87 % Favored : 79.85 % 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: -1.02 (0.20), residues: 1699 helix: 0.88 (0.50), residues: 119 sheet: -0.36 (0.18), residues: 769 loop : -1.16 (0.22), residues: 811 *********************** 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 375 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 361 time to evaluate : 1.896 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 outliers start: 14 outliers final: 11 residues processed: 364 average time/residue: 0.6175 time to fit residues: 308.4054 Evaluate side-chains 364 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 353 time to evaluate : 1.880 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4459 time to fit residues: 10.1831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 168 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 134 optimal weight: 0.0980 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN C 223 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 13235 Z= 0.357 Angle : 0.600 5.684 17973 Z= 0.332 Chirality : 0.045 0.188 1885 Planarity : 0.004 0.056 2429 Dihedral : 4.451 20.250 1883 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.05 % Allowed : 19.77 % Favored : 79.17 % 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: 0.97 (0.50), residues: 119 sheet: -0.36 (0.18), residues: 769 loop : -1.20 (0.21), residues: 811 ********************** 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 373 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 362 time to evaluate : 2.148 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 outliers start: 11 outliers final: 7 residues processed: 367 average time/residue: 0.6443 time to fit residues: 328.0083 Evaluate side-chains 358 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 351 time to evaluate : 1.899 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3435 time to fit residues: 6.4200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 19 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 134 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.201053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.139437 restraints weight = 105530.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144141 restraints weight = 28170.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.145775 restraints weight = 11309.135| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 44 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.5425 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= 0.179 Angle : 0.550 5.613 17973 Z= 0.301 Chirality : 0.044 0.172 1885 Planarity : 0.004 0.061 2429 Dihedral : 4.249 20.338 1883 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.53 % Allowed : 21.35 % 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: -0.74 (0.20), residues: 1699 helix: 1.19 (0.51), residues: 119 sheet: -0.13 (0.18), residues: 766 loop : -1.05 (0.22), residues: 814 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6584.74 seconds wall clock time: 116 minutes 58.68 seconds (7018.68 seconds total)