Starting phenix.real_space_refine on Thu Jul 2 09:59:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226.map" model { file = "/net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eo4_31226/07_2026/7eo4_31226_neut.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.078 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 58 5.16 5 C 5311 2.51 5 N 1399 2.21 5 O 1531 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2247 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'TRANS': 150} Chain breaks: 4 Chain: "C" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'J8C': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.57, per 1000 atoms: 0.19 Number of scatterers: 8302 At special positions: 0 Unit cell: (93.5, 123.2, 129.8, 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 58 16.00 F 3 9.00 O 1531 8.00 N 1399 7.00 C 5311 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.52 Conformation dependent library (CDL) restraints added in 435.1 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.4% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.964A pdb=" N VAL A 26 " --> pdb=" O TYR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 72 removed outlier: 3.630A pdb=" N LYS A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.615A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 109 Processing helix chain 'A' and resid 113 through 146 removed outlier: 4.004A pdb=" N ALA A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 176 removed outlier: 3.644A pdb=" N GLY A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.539A pdb=" N SER A 190 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N CYS A 191 " --> pdb=" O LEU A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 199 through 233 removed outlier: 3.890A pdb=" N ILE A 203 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 281 removed outlier: 3.938A pdb=" N ILE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Proline residue: A 271 - end of helix removed outlier: 3.903A pdb=" N VAL A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 293 removed outlier: 4.125A pdb=" N ALA A 293 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 314 removed outlier: 3.800A pdb=" N ALA A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Proline residue: A 308 - end of helix removed outlier: 3.715A pdb=" N THR A 314 " --> pdb=" O ILE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 323 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.830A pdb=" N LYS B 10 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.760A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.578A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'D' and resid 8 through 24 removed outlier: 4.062A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.770A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.918A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.558A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.557A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 4.284A pdb=" N VAL B 185 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.899A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.676A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 153 removed outlier: 3.886A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 158 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLN C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.548A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 201 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.601A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE C 253 " --> pdb=" O PHE C 241 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 275 removed outlier: 4.074A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 287 " --> pdb=" O ASN C 295 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.173A pdb=" N GLY E 16 " --> pdb=" O SER E 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.338A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.338A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.505A pdb=" N CYS E 147 " --> pdb=" O PHE E 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.521A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2587 1.34 - 1.46: 1992 1.46 - 1.58: 3806 1.58 - 1.71: 3 1.71 - 1.83: 81 Bond restraints: 8469 Sorted by residual: bond pdb=" C07 J8C A 401 " pdb=" C09 J8C A 401 " ideal model delta sigma weight residual 1.481 1.622 -0.141 2.00e-02 2.50e+03 4.96e+01 bond pdb=" C12 J8C A 401 " pdb=" C13 J8C A 401 " ideal model delta sigma weight residual 1.497 1.584 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C34 J8C A 401 " pdb=" N31 J8C A 401 " ideal model delta sigma weight residual 1.467 1.544 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C25 J8C A 401 " pdb=" F26 J8C A 401 " ideal model delta sigma weight residual 1.338 1.408 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C32 J8C A 401 " pdb=" N31 J8C A 401 " ideal model delta sigma weight residual 1.467 1.536 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 8464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 11081 2.32 - 4.63: 323 4.63 - 6.95: 50 6.95 - 9.26: 12 9.26 - 11.58: 6 Bond angle restraints: 11472 Sorted by residual: angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" CB MET E 180 " ideal model delta sigma weight residual 114.17 108.76 5.41 1.14e+00 7.69e-01 2.25e+01 angle pdb=" N ASP C 303 " pdb=" CA ASP C 303 " pdb=" C ASP C 303 " ideal model delta sigma weight residual 107.48 117.67 -10.19 2.29e+00 1.91e-01 1.98e+01 angle pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" C ASP E 211 " ideal model delta sigma weight residual 110.80 101.34 9.46 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N PHE C 292 " pdb=" CA PHE C 292 " pdb=" CB PHE C 292 " ideal model delta sigma weight residual 114.17 109.11 5.06 1.14e+00 7.69e-01 1.97e+01 angle pdb=" C ASP C 303 " pdb=" CA ASP C 303 " pdb=" CB ASP C 303 " ideal model delta sigma weight residual 111.77 105.30 6.47 1.52e+00 4.33e-01 1.81e+01 ... (remaining 11467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 4739 23.45 - 46.91: 243 46.91 - 70.36: 24 70.36 - 93.81: 12 93.81 - 117.27: 5 Dihedral angle restraints: 5023 sinusoidal: 1958 harmonic: 3065 Sorted by residual: dihedral pdb=" C ASP E 211 " pdb=" N ASP E 211 " pdb=" CA ASP E 211 " pdb=" CB ASP E 211 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" CA THR B 187 " pdb=" C THR B 187 " pdb=" N HIS B 188 " pdb=" CA HIS B 188 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1139 0.080 - 0.160: 174 0.160 - 0.240: 9 0.240 - 0.320: 1 0.320 - 0.400: 2 Chirality restraints: 1325 Sorted by residual: chirality pdb=" C33 J8C A 401 " pdb=" C32 J8C A 401 " pdb=" C34 J8C A 401 " pdb=" C35 J8C A 401 " both_signs ideal model delta sigma weight residual False 2.65 3.05 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CA ASP E 211 " pdb=" N ASP E 211 " pdb=" C ASP E 211 " pdb=" CB ASP E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ALA E 209 " pdb=" N ALA E 209 " pdb=" C ALA E 209 " pdb=" CB ALA E 209 " both_signs ideal model delta sigma weight residual False 2.48 2.74 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1322 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 292 " -0.291 9.50e-02 1.11e+02 1.31e-01 1.05e+01 pdb=" NE ARG A 292 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 292 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 292 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 292 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO C 236 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 177 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.61e+00 pdb=" N PRO A 178 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.039 5.00e-02 4.00e+02 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1247 2.76 - 3.29: 7608 3.29 - 3.83: 12487 3.83 - 4.36: 14905 4.36 - 4.90: 26004 Nonbonded interactions: 62251 Sorted by model distance: nonbonded pdb=" N GLY C 144 " pdb=" OD1 ASP C 163 " model vdw 2.220 3.120 nonbonded pdb=" O GLY E 197 " pdb=" OG1 THR E 198 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR C 86 " pdb=" OD1 ASN C 88 " model vdw 2.244 3.040 nonbonded pdb=" O LEU C 30 " pdb=" OG1 THR C 34 " model vdw 2.274 3.040 nonbonded pdb=" O ASP C 163 " pdb=" OG1 THR C 164 " model vdw 2.297 3.040 ... (remaining 62246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.970 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.008 0.141 8472 Z= 0.346 Angle : 0.974 11.576 11478 Z= 0.532 Chirality : 0.057 0.400 1325 Planarity : 0.007 0.131 1424 Dihedral : 14.968 117.267 3034 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1033 helix: 1.19 (0.29), residues: 312 sheet: -1.83 (0.30), residues: 239 loop : -1.84 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 304 TYR 0.023 0.003 TYR A 31 PHE 0.040 0.003 PHE C 151 TRP 0.025 0.003 TRP C 63 HIS 0.011 0.002 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.35 ( 8469) covalent geometry : angle 0.97421 / 0.53 (11472) SS BOND : bond 0.00636 / 0.32 ( 3) SS BOND : angle 1.02970 / 0.61 ( 6) hydrogen bonds : bond 0.20896 / 13.60 ( 369) hydrogen bonds : angle 6.97145 / 5.09 ( 1035) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.347 Fit side-chains REVERT: E 18 ARG cc_start: 0.7797 (tpp80) cc_final: 0.7583 (ttt90) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.4694 time to fit residues: 86.9125 Evaluate side-chains 148 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 ASN C 220 GLN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.229895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.196480 restraints weight = 9405.396| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.82 r_work: 0.3656 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8472 Z= 0.134 Angle : 0.611 6.648 11478 Z= 0.324 Chirality : 0.043 0.154 1325 Planarity : 0.004 0.061 1424 Dihedral : 8.253 77.151 1181 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.88 % Allowed : 11.05 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.26), residues: 1033 helix: 2.00 (0.29), residues: 318 sheet: -1.04 (0.29), residues: 274 loop : -1.72 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 206 TYR 0.011 0.001 TYR E 103 PHE 0.020 0.002 PHE C 151 TRP 0.019 0.002 TRP C 82 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8469) covalent geometry : angle 0.61069 / 0.32 (11472) SS BOND : bond 0.00493 / 0.25 ( 3) SS BOND : angle 0.59847 / 0.35 ( 6) hydrogen bonds : bond 0.05896 / 3.88 ( 369) hydrogen bonds : angle 4.87642 / 3.52 ( 1035) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.311 Fit side-chains REVERT: C 340 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7431 (p0) outliers start: 17 outliers final: 7 residues processed: 163 average time/residue: 0.4521 time to fit residues: 79.1102 Evaluate side-chains 159 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 151 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 340 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 ASN C 220 GLN D 18 GLN E 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.229872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.194770 restraints weight = 9395.172| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.81 r_work: 0.3648 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8472 Z= 0.129 Angle : 0.569 6.335 11478 Z= 0.304 Chirality : 0.042 0.156 1325 Planarity : 0.004 0.056 1424 Dihedral : 7.271 71.258 1181 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.87 % Allowed : 14.03 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 1033 helix: 2.35 (0.29), residues: 319 sheet: -0.75 (0.30), residues: 262 loop : -1.70 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 18 TYR 0.011 0.001 TYR A 295 PHE 0.019 0.001 PHE C 151 TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 8469) covalent geometry : angle 0.56883 / 0.30 (11472) SS BOND : bond 0.00441 / 0.22 ( 3) SS BOND : angle 0.47880 / 0.28 ( 6) hydrogen bonds : bond 0.05376 / 3.53 ( 369) hydrogen bonds : angle 4.57458 / 3.30 ( 1035) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.193 Fit side-chains REVERT: C 44 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: C 200 VAL cc_start: 0.8673 (m) cc_final: 0.8253 (t) outliers start: 26 outliers final: 15 residues processed: 167 average time/residue: 0.4001 time to fit residues: 72.0288 Evaluate side-chains 166 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 58 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 75 GLN C 176 GLN C 220 GLN E 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.228497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.193624 restraints weight = 9456.941| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.92 r_work: 0.3621 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8472 Z= 0.151 Angle : 0.600 6.303 11478 Z= 0.321 Chirality : 0.042 0.160 1325 Planarity : 0.004 0.054 1424 Dihedral : 6.858 65.364 1181 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.31 % Allowed : 17.35 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.27), residues: 1033 helix: 2.41 (0.29), residues: 319 sheet: -0.61 (0.31), residues: 260 loop : -1.71 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 320 TYR 0.012 0.002 TYR E 103 PHE 0.023 0.002 PHE C 151 TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 8469) covalent geometry : angle 0.59990 / 0.32 (11472) SS BOND : bond 0.00466 / 0.24 ( 3) SS BOND : angle 0.50127 / 0.29 ( 6) hydrogen bonds : bond 0.05771 / 3.77 ( 369) hydrogen bonds : angle 4.58938 / 3.30 ( 1035) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.310 Fit side-chains REVERT: C 44 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7031 (tm-30) outliers start: 30 outliers final: 17 residues processed: 165 average time/residue: 0.3968 time to fit residues: 70.4441 Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 0.0040 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.229529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.195024 restraints weight = 9445.470| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 1.84 r_work: 0.3637 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8472 Z= 0.128 Angle : 0.563 7.330 11478 Z= 0.299 Chirality : 0.041 0.150 1325 Planarity : 0.004 0.052 1424 Dihedral : 6.418 59.949 1181 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.20 % Allowed : 18.56 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 1033 helix: 2.57 (0.29), residues: 321 sheet: -0.55 (0.30), residues: 267 loop : -1.60 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 320 TYR 0.011 0.001 TYR A 295 PHE 0.019 0.001 PHE C 151 TRP 0.015 0.001 TRP C 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 8469) covalent geometry : angle 0.56281 / 0.30 (11472) SS BOND : bond 0.00411 / 0.21 ( 3) SS BOND : angle 0.44166 / 0.25 ( 6) hydrogen bonds : bond 0.05118 / 3.36 ( 369) hydrogen bonds : angle 4.41916 / 3.18 ( 1035) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: C 44 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.6947 (tm-30) REVERT: C 200 VAL cc_start: 0.8610 (m) cc_final: 0.8215 (t) REVERT: E 128 MET cc_start: 0.6977 (OUTLIER) cc_final: 0.5634 (mmm) outliers start: 29 outliers final: 16 residues processed: 163 average time/residue: 0.4356 time to fit residues: 76.2617 Evaluate side-chains 165 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 128 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 220 GLN C 237 ASN C 239 ASN C 340 ASN E 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.227078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.186374 restraints weight = 9271.817| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.83 r_work: 0.3581 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8472 Z= 0.172 Angle : 0.629 8.270 11478 Z= 0.336 Chirality : 0.043 0.155 1325 Planarity : 0.005 0.052 1424 Dihedral : 6.487 58.149 1181 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.65 % Allowed : 18.78 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.27), residues: 1033 helix: 2.45 (0.29), residues: 320 sheet: -0.52 (0.31), residues: 255 loop : -1.67 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 320 TYR 0.013 0.002 TYR E 95 PHE 0.027 0.002 PHE C 151 TRP 0.015 0.002 TRP C 82 HIS 0.006 0.001 HIS B 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 ( 8469) covalent geometry : angle 0.62950 / 0.34 (11472) SS BOND : bond 0.00511 / 0.26 ( 3) SS BOND : angle 0.54795 / 0.31 ( 6) hydrogen bonds : bond 0.06154 / 4.01 ( 369) hydrogen bonds : angle 4.60565 / 3.29 ( 1035) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.308 Fit side-chains REVERT: A 75 LYS cc_start: 0.8005 (mppt) cc_final: 0.7371 (mttm) REVERT: A 319 ARG cc_start: 0.6531 (mtm-85) cc_final: 0.6172 (mtm-85) REVERT: B 209 LYS cc_start: 0.4730 (mmtp) cc_final: 0.4361 (ptpt) REVERT: C 44 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: C 280 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6366 (mtpp) REVERT: E 18 ARG cc_start: 0.8318 (tpp80) cc_final: 0.8089 (tpp80) REVERT: E 128 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.5627 (mmm) outliers start: 33 outliers final: 20 residues processed: 164 average time/residue: 0.4003 time to fit residues: 70.7620 Evaluate side-chains 168 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 280 LYS Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 128 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 38 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 12 optimal weight: 5.9990 chunk 81 optimal weight: 0.0770 chunk 77 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 220 GLN C 239 ASN E 3 GLN E 182 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.231725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.197262 restraints weight = 9457.678| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.86 r_work: 0.3673 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8472 Z= 0.107 Angle : 0.533 9.442 11478 Z= 0.279 Chirality : 0.040 0.146 1325 Planarity : 0.004 0.047 1424 Dihedral : 5.891 58.540 1181 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.09 % Allowed : 20.11 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.27), residues: 1033 helix: 2.86 (0.29), residues: 318 sheet: -0.47 (0.31), residues: 263 loop : -1.41 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.012 0.001 TYR A 295 PHE 0.014 0.001 PHE C 199 TRP 0.015 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 8469) covalent geometry : angle 0.53300 / 0.28 (11472) SS BOND : bond 0.00343 / 0.17 ( 3) SS BOND : angle 0.40137 / 0.22 ( 6) hydrogen bonds : bond 0.04331 / 2.86 ( 369) hydrogen bonds : angle 4.23017 / 3.05 ( 1035) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.226 Fit side-chains REVERT: A 65 PHE cc_start: 0.7695 (t80) cc_final: 0.6962 (t80) REVERT: A 312 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7281 (m) REVERT: A 319 ARG cc_start: 0.6392 (mtm-85) cc_final: 0.6025 (mtm-85) REVERT: C 44 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: C 200 VAL cc_start: 0.8633 (m) cc_final: 0.8200 (t) REVERT: D 21 MET cc_start: 0.6142 (mpm) cc_final: 0.5667 (mtp) REVERT: E 206 ARG cc_start: 0.7034 (mtm-85) cc_final: 0.6080 (mmm-85) outliers start: 28 outliers final: 13 residues processed: 163 average time/residue: 0.4111 time to fit residues: 72.3445 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 0.0040 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN C 220 GLN C 239 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.231594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.195900 restraints weight = 9407.120| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.91 r_work: 0.3664 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8472 Z= 0.111 Angle : 0.542 7.852 11478 Z= 0.283 Chirality : 0.040 0.148 1325 Planarity : 0.004 0.044 1424 Dihedral : 5.681 56.297 1181 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.54 % Allowed : 21.66 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 1033 helix: 2.93 (0.29), residues: 318 sheet: -0.45 (0.31), residues: 263 loop : -1.38 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 320 TYR 0.014 0.001 TYR E 178 PHE 0.016 0.001 PHE C 151 TRP 0.014 0.001 TRP C 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 8469) covalent geometry : angle 0.54213 / 0.28 (11472) SS BOND : bond 0.00346 / 0.17 ( 3) SS BOND : angle 0.39781 / 0.22 ( 6) hydrogen bonds : bond 0.04376 / 2.86 ( 369) hydrogen bonds : angle 4.20622 / 3.03 ( 1035) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.333 Fit side-chains REVERT: A 65 PHE cc_start: 0.7782 (t80) cc_final: 0.6961 (t80) REVERT: A 312 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7292 (m) REVERT: C 44 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: C 200 VAL cc_start: 0.8652 (m) cc_final: 0.8214 (t) REVERT: E 206 ARG cc_start: 0.7030 (mtm-85) cc_final: 0.6087 (mmm-85) outliers start: 23 outliers final: 15 residues processed: 154 average time/residue: 0.4387 time to fit residues: 72.7542 Evaluate side-chains 158 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 28 optimal weight: 0.0070 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN C 220 GLN C 239 ASN E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.229453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.194457 restraints weight = 9313.515| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.77 r_work: 0.3631 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8472 Z= 0.138 Angle : 0.592 11.306 11478 Z= 0.310 Chirality : 0.042 0.148 1325 Planarity : 0.004 0.042 1424 Dihedral : 5.753 52.670 1181 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.32 % Allowed : 22.10 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.27), residues: 1033 helix: 2.81 (0.29), residues: 318 sheet: -0.50 (0.30), residues: 266 loop : -1.44 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.015 0.002 TYR E 178 PHE 0.021 0.001 PHE C 151 TRP 0.014 0.002 TRP A 182 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8469) covalent geometry : angle 0.59194 / 0.31 (11472) SS BOND : bond 0.00409 / 0.21 ( 3) SS BOND : angle 0.43227 / 0.24 ( 6) hydrogen bonds : bond 0.05151 / 3.36 ( 369) hydrogen bonds : angle 4.37256 / 3.14 ( 1035) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.327 Fit side-chains REVERT: C 44 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.6952 (tm-30) REVERT: D 21 MET cc_start: 0.5981 (mpm) cc_final: 0.5617 (mtp) REVERT: E 206 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6282 (mmm-85) outliers start: 21 outliers final: 16 residues processed: 151 average time/residue: 0.4631 time to fit residues: 75.2572 Evaluate side-chains 155 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 91 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN C 220 GLN C 239 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.229007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.192833 restraints weight = 9352.199| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.90 r_work: 0.3613 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8472 Z= 0.141 Angle : 0.603 11.154 11478 Z= 0.315 Chirality : 0.042 0.150 1325 Planarity : 0.004 0.043 1424 Dihedral : 5.653 48.942 1181 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.32 % Allowed : 22.10 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.27), residues: 1033 helix: 2.78 (0.28), residues: 318 sheet: -0.43 (0.31), residues: 254 loop : -1.49 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.018 0.002 TYR E 178 PHE 0.021 0.001 PHE C 151 TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 8469) covalent geometry : angle 0.60277 / 0.31 (11472) SS BOND : bond 0.00423 / 0.21 ( 3) SS BOND : angle 0.43985 / 0.24 ( 6) hydrogen bonds : bond 0.05244 / 3.42 ( 369) hydrogen bonds : angle 4.39258 / 3.15 ( 1035) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.376 Fit side-chains REVERT: A 319 ARG cc_start: 0.6448 (mtm-85) cc_final: 0.6049 (mtm-85) REVERT: B 209 LYS cc_start: 0.4644 (mmtp) cc_final: 0.4438 (tppt) REVERT: C 44 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.6965 (tm-30) REVERT: D 21 MET cc_start: 0.6000 (mpm) cc_final: 0.5601 (mtp) REVERT: E 206 ARG cc_start: 0.7205 (mtm-85) cc_final: 0.6274 (mmm-85) outliers start: 21 outliers final: 18 residues processed: 153 average time/residue: 0.4721 time to fit residues: 77.6720 Evaluate side-chains 160 residues out of total 911 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 126 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 22 ASN C 220 GLN C 239 ASN ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.229145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.195982 restraints weight = 9366.220| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 1.76 r_work: 0.3639 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8472 Z= 0.137 Angle : 0.595 10.875 11478 Z= 0.311 Chirality : 0.042 0.150 1325 Planarity : 0.004 0.042 1424 Dihedral : 5.470 48.716 1181 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.10 % Allowed : 22.32 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.27), residues: 1033 helix: 2.80 (0.29), residues: 318 sheet: -0.56 (0.30), residues: 266 loop : -1.44 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 320 TYR 0.018 0.002 TYR E 178 PHE 0.021 0.001 PHE C 151 TRP 0.014 0.002 TRP C 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8469) covalent geometry : angle 0.59553 / 0.31 (11472) SS BOND : bond 0.00414 / 0.21 ( 3) SS BOND : angle 0.44478 / 0.24 ( 6) hydrogen bonds : bond 0.05160 / 3.36 ( 369) hydrogen bonds : angle 4.37569 / 3.14 ( 1035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2647.64 seconds wall clock time: 45 minutes 53.76 seconds (2753.76 seconds total)