Starting phenix.real_space_refine on Tue Mar 3 20:35:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmu_30410/03_2026/7cmu_30410.map" } resolution = 3.0 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= 0.010 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5571 2.51 5 N 1491 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8771 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "C" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2128 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 1 Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'G6L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.03, per 1000 atoms: 0.23 Number of scatterers: 8771 At special positions: 0 Unit cell: (105.456, 127.764, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1641 8.00 N 1491 7.00 C 5571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.03 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: 0.71 Conformation dependent library (CDL) restraints added in 245.5 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 40.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.284A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.806A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.700A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.786A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 352 removed outlier: 3.939A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.706A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.553A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.974A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.749A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 57 Processing helix chain 'R' and resid 58 through 61 Processing helix chain 'R' and resid 62 through 82 removed outlier: 4.138A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'R' and resid 99 through 134 Processing helix chain 'R' and resid 134 through 139 removed outlier: 4.021A pdb=" N TYR R 138 " --> pdb=" O MET R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 142 No H-bonds generated for 'chain 'R' and resid 140 through 142' Processing helix chain 'R' and resid 143 through 170 Proline residue: R 167 - end of helix removed outlier: 3.588A pdb=" N PHE R 170 " --> pdb=" O CYS R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 197 removed outlier: 3.596A pdb=" N ILE R 190 " --> pdb=" O PRO R 186 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR R 191 " --> pdb=" O ASP R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 322 through 355 Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 361 through 385 removed outlier: 3.722A pdb=" N ASN R 375 " --> pdb=" O LEU R 371 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 400 removed outlier: 3.713A pdb=" N CYS R 400 " --> pdb=" O LYS R 396 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.604A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.597A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.879A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.767A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.724A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.760A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.522A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.023A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.477A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.729A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.137A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.137A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 456 hydrogen bonds defined for protein. 1284 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: 1.40 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2827 1.34 - 1.46: 1999 1.46 - 1.58: 4025 1.58 - 1.69: 2 1.69 - 1.81: 97 Bond restraints: 8950 Sorted by residual: bond pdb=" C7 G6L R 500 " pdb=" N3 G6L R 500 " ideal model delta sigma weight residual 1.357 1.451 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C4 G6L R 500 " pdb=" C6 G6L R 500 " ideal model delta sigma weight residual 1.527 1.609 -0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 G6L R 500 " pdb=" C6 G6L R 500 " ideal model delta sigma weight residual 1.528 1.599 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C7 G6L R 500 " pdb=" N1 G6L R 500 " ideal model delta sigma weight residual 1.295 1.352 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C1 G6L R 500 " pdb=" C3 G6L R 500 " ideal model delta sigma weight residual 1.490 1.443 0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 8945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 12074 2.64 - 5.28: 47 5.28 - 7.93: 4 7.93 - 10.57: 1 10.57 - 13.21: 5 Bond angle restraints: 12131 Sorted by residual: angle pdb=" C2 G6L R 500 " pdb=" N1 G6L R 500 " pdb=" C7 G6L R 500 " ideal model delta sigma weight residual 110.90 124.11 -13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C1 G6L R 500 " pdb=" C3 G6L R 500 " pdb=" C5 G6L R 500 " ideal model delta sigma weight residual 109.78 121.52 -11.74 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C4 G6L R 500 " pdb=" C2 G6L R 500 " pdb=" N1 G6L R 500 " ideal model delta sigma weight residual 121.65 133.19 -11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" N1 G6L R 500 " pdb=" C7 G6L R 500 " pdb=" S G6L R 500 " ideal model delta sigma weight residual 114.53 103.61 10.92 3.00e+00 1.11e-01 1.33e+01 angle pdb=" C1 G6L R 500 " pdb=" C2 G6L R 500 " pdb=" N1 G6L R 500 " ideal model delta sigma weight residual 116.52 105.71 10.81 3.00e+00 1.11e-01 1.30e+01 ... (remaining 12126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4927 17.66 - 35.32: 331 35.32 - 52.99: 43 52.99 - 70.65: 10 70.65 - 88.31: 9 Dihedral angle restraints: 5320 sinusoidal: 2060 harmonic: 3260 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 62.20 30.80 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" CA LEU R 81 " pdb=" C LEU R 81 " pdb=" N VAL R 82 " pdb=" CA VAL R 82 " ideal model delta harmonic sigma weight residual -180.00 -162.38 -17.62 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB GLU C 47 " pdb=" CG GLU C 47 " pdb=" CD GLU C 47 " pdb=" OE1 GLU C 47 " ideal model delta sinusoidal sigma weight residual 0.00 -88.31 88.31 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 5317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 903 0.028 - 0.057: 314 0.057 - 0.085: 94 0.085 - 0.114: 52 0.114 - 0.142: 29 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CA MET R 83 " pdb=" N MET R 83 " pdb=" C MET R 83 " pdb=" CB MET R 83 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE R 183 " pdb=" N ILE R 183 " pdb=" C ILE R 183 " pdb=" CB ILE R 183 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1389 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 185 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO R 186 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO R 186 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 186 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 13 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C ARG C 13 " -0.035 2.00e-02 2.50e+03 pdb=" O ARG C 13 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 14 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 379 " -0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO R 380 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 380 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 380 " -0.018 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 61 2.58 - 3.16: 7285 3.16 - 3.74: 13289 3.74 - 4.32: 18495 4.32 - 4.90: 31625 Nonbonded interactions: 70755 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 1.996 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 1.999 3.040 nonbonded pdb=" OG SER E 146 " pdb=" OE2 GLU E 246 " model vdw 2.022 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.055 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.100 3.120 ... (remaining 70750 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: 0.680 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.040 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 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:10.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 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 0.094 8953 Z= 0.144 Angle : 0.509 13.208 12137 Z= 0.268 Chirality : 0.039 0.142 1392 Planarity : 0.003 0.065 1528 Dihedral : 12.331 88.310 3207 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.96 (0.26), residues: 1105 helix: 3.73 (0.26), residues: 387 sheet: 1.61 (0.32), residues: 257 loop : 0.65 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.006 0.001 TYR A 230 PHE 0.007 0.000 PHE E 68 TRP 0.005 0.000 TRP B 82 HIS 0.005 0.000 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8950) covalent geometry : angle 0.50912 (12131) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.28033 ( 6) hydrogen bonds : bond 0.17251 ( 452) hydrogen bonds : angle 6.12246 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.328 Fit side-chains REVERT: A 32 ARG cc_start: 0.7110 (mtm180) cc_final: 0.6710 (mmt180) REVERT: A 248 LYS cc_start: 0.7875 (tppt) cc_final: 0.7366 (pptt) REVERT: R 125 SER cc_start: 0.8235 (t) cc_final: 0.7857 (m) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.4571 time to fit residues: 104.4752 Evaluate side-chains 152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS B 44 GLN B 62 HIS B 110 ASN B 220 GLN E 194 ASN R 65 ASN R 144 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.202993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.144693 restraints weight = 9437.358| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.84 r_work: 0.3489 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8953 Z= 0.146 Angle : 0.568 7.259 12137 Z= 0.296 Chirality : 0.044 0.155 1392 Planarity : 0.004 0.047 1528 Dihedral : 4.084 43.585 1228 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.74 % Allowed : 11.43 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 2.42 (0.25), residues: 1105 helix: 3.37 (0.25), residues: 392 sheet: 1.10 (0.30), residues: 272 loop : 0.33 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.016 0.001 TYR E 59 PHE 0.020 0.002 PHE E 68 TRP 0.011 0.001 TRP B 99 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 8950) covalent geometry : angle 0.56808 (12131) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.96869 ( 6) hydrogen bonds : bond 0.03858 ( 452) hydrogen bonds : angle 4.43308 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7097 (mmt180) REVERT: A 248 LYS cc_start: 0.8001 (tppt) cc_final: 0.7513 (pptt) REVERT: A 269 ASN cc_start: 0.6732 (m-40) cc_final: 0.6352 (m110) REVERT: A 349 LYS cc_start: 0.7403 (mttp) cc_final: 0.7124 (mptp) REVERT: B 217 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7524 (ppp) REVERT: E 140 MET cc_start: 0.8883 (mmm) cc_final: 0.8452 (mmt) REVERT: E 218 ARG cc_start: 0.8022 (ptp90) cc_final: 0.7688 (ptp90) REVERT: R 113 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6927 (mmt) outliers start: 36 outliers final: 12 residues processed: 181 average time/residue: 0.5186 time to fit residues: 100.2444 Evaluate side-chains 149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN B 237 ASN E 194 ASN R 65 ASN R 120 ASN R 139 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.196471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141056 restraints weight = 9469.550| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.70 r_work: 0.3450 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8953 Z= 0.197 Angle : 0.606 9.789 12137 Z= 0.316 Chirality : 0.045 0.221 1392 Planarity : 0.004 0.038 1528 Dihedral : 4.437 38.898 1228 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.41 % Allowed : 14.45 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.84 (0.25), residues: 1105 helix: 2.99 (0.25), residues: 392 sheet: 0.56 (0.29), residues: 284 loop : 0.04 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.019 0.002 TYR E 59 PHE 0.033 0.002 PHE E 68 TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 8950) covalent geometry : angle 0.60527 (12131) SS BOND : bond 0.00494 ( 3) SS BOND : angle 1.05887 ( 6) hydrogen bonds : bond 0.04170 ( 452) hydrogen bonds : angle 4.41494 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.198 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7544 (mtm180) cc_final: 0.7324 (mtm180) REVERT: A 248 LYS cc_start: 0.7931 (tppt) cc_final: 0.7572 (pptt) REVERT: B 217 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7533 (ppp) REVERT: B 325 MET cc_start: 0.7892 (mmm) cc_final: 0.7662 (mmt) REVERT: E 23 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8398 (p) REVERT: E 82 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7172 (mm-40) REVERT: E 218 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7771 (ptp90) REVERT: R 113 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6951 (mmm) REVERT: R 134 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4855 (ttp) outliers start: 52 outliers final: 24 residues processed: 197 average time/residue: 0.5318 time to fit residues: 111.6561 Evaluate side-chains 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 113 MET Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.6980 chunk 72 optimal weight: 0.0570 chunk 74 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 333 GLN B 237 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.201475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.142833 restraints weight = 9623.246| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.89 r_work: 0.3474 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8953 Z= 0.109 Angle : 0.526 7.775 12137 Z= 0.274 Chirality : 0.042 0.204 1392 Planarity : 0.003 0.035 1528 Dihedral : 4.188 36.709 1228 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.53 % Allowed : 18.09 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.95 (0.25), residues: 1105 helix: 3.21 (0.25), residues: 392 sheet: 0.65 (0.30), residues: 274 loop : -0.04 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 18 TYR 0.011 0.001 TYR E 59 PHE 0.023 0.001 PHE E 68 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8950) covalent geometry : angle 0.52565 (12131) SS BOND : bond 0.00291 ( 3) SS BOND : angle 0.43601 ( 6) hydrogen bonds : bond 0.03232 ( 452) hydrogen bonds : angle 4.09250 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.325 Fit side-chains REVERT: A 349 LYS cc_start: 0.7439 (mttp) cc_final: 0.7227 (mptp) REVERT: B 214 ARG cc_start: 0.8086 (ptp-110) cc_final: 0.7750 (mtm110) REVERT: B 217 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (ppp) REVERT: B 325 MET cc_start: 0.7895 (mmm) cc_final: 0.7679 (mmt) REVERT: E 6 GLU cc_start: 0.8051 (mp0) cc_final: 0.7795 (mp0) REVERT: E 82 GLN cc_start: 0.7432 (mm-40) cc_final: 0.7114 (mm-40) REVERT: E 218 ARG cc_start: 0.7963 (ptp90) cc_final: 0.7708 (ptp90) REVERT: R 61 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7707 (mp10) REVERT: R 134 MET cc_start: 0.4657 (OUTLIER) cc_final: 0.4448 (ttp) REVERT: R 149 ARG cc_start: 0.6716 (tpt-90) cc_final: 0.4456 (ttp-110) REVERT: R 389 GLU cc_start: 0.7104 (mp0) cc_final: 0.6799 (pm20) outliers start: 34 outliers final: 12 residues processed: 188 average time/residue: 0.5211 time to fit residues: 104.6432 Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 204 GLN A 241 ASN A 269 ASN A 304 GLN B 75 GLN B 237 ASN R 65 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.188990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.132176 restraints weight = 9703.953| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.58 r_work: 0.3335 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 8953 Z= 0.360 Angle : 0.763 11.609 12137 Z= 0.400 Chirality : 0.051 0.210 1392 Planarity : 0.005 0.071 1528 Dihedral : 5.136 47.260 1228 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 6.03 % Allowed : 17.57 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.12 (0.24), residues: 1105 helix: 2.50 (0.25), residues: 384 sheet: 0.26 (0.30), residues: 275 loop : -0.49 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 27 TYR 0.025 0.003 TYR A 230 PHE 0.047 0.003 PHE E 68 TRP 0.019 0.003 TRP B 82 HIS 0.012 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00862 ( 8950) covalent geometry : angle 0.76210 (12131) SS BOND : bond 0.00560 ( 3) SS BOND : angle 1.70448 ( 6) hydrogen bonds : bond 0.05091 ( 452) hydrogen bonds : angle 4.86437 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7491 (mtm110) cc_final: 0.7198 (mmt180) REVERT: A 248 LYS cc_start: 0.8165 (tppt) cc_final: 0.7754 (pptt) REVERT: B 172 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6110 (pm20) REVERT: B 173 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8373 (p) REVERT: B 214 ARG cc_start: 0.8072 (ptp-110) cc_final: 0.7864 (mtm110) REVERT: E 82 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7463 (mm-40) REVERT: E 218 ARG cc_start: 0.7967 (ptp90) cc_final: 0.7631 (ptp90) REVERT: R 61 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: R 132 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6337 (t) REVERT: R 134 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5692 (ttp) outliers start: 58 outliers final: 32 residues processed: 204 average time/residue: 0.4815 time to fit residues: 104.9916 Evaluate side-chains 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 132 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 134 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 348 THR Chi-restraints excluded: chain R residue 351 LEU Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 10.0000 chunk 102 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.197984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.140732 restraints weight = 9594.940| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.76 r_work: 0.3450 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8953 Z= 0.119 Angle : 0.562 8.272 12137 Z= 0.292 Chirality : 0.042 0.212 1392 Planarity : 0.004 0.039 1528 Dihedral : 4.496 43.945 1228 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.01 % Allowed : 21.21 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.53 (0.25), residues: 1105 helix: 3.02 (0.25), residues: 384 sheet: 0.29 (0.30), residues: 287 loop : -0.30 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 32 TYR 0.022 0.001 TYR A 230 PHE 0.024 0.001 PHE E 68 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8950) covalent geometry : angle 0.56243 (12131) SS BOND : bond 0.00275 ( 3) SS BOND : angle 0.44660 ( 6) hydrogen bonds : bond 0.03327 ( 452) hydrogen bonds : angle 4.31441 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 349 LYS cc_start: 0.7567 (mttp) cc_final: 0.7360 (mttp) REVERT: B 130 GLU cc_start: 0.7691 (mp0) cc_final: 0.7462 (mp0) REVERT: B 246 ASP cc_start: 0.8513 (m-30) cc_final: 0.8261 (m-30) REVERT: E 82 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7295 (mm-40) REVERT: E 87 ARG cc_start: 0.7242 (mpp-170) cc_final: 0.6988 (mpt-90) REVERT: E 218 ARG cc_start: 0.7900 (ptp90) cc_final: 0.7638 (ptp90) REVERT: R 61 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (mp10) outliers start: 29 outliers final: 14 residues processed: 180 average time/residue: 0.5078 time to fit residues: 97.6771 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 89 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 241 ASN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.193975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.134884 restraints weight = 9628.422| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.86 r_work: 0.3401 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8953 Z= 0.182 Angle : 0.618 9.112 12137 Z= 0.322 Chirality : 0.044 0.205 1392 Planarity : 0.004 0.041 1528 Dihedral : 4.610 43.422 1228 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.64 % Allowed : 21.10 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.31 (0.25), residues: 1105 helix: 2.80 (0.25), residues: 384 sheet: 0.17 (0.30), residues: 290 loop : -0.39 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 27 TYR 0.020 0.002 TYR A 230 PHE 0.024 0.002 PHE E 68 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8950) covalent geometry : angle 0.61805 (12131) SS BOND : bond 0.00322 ( 3) SS BOND : angle 1.09507 ( 6) hydrogen bonds : bond 0.03833 ( 452) hydrogen bonds : angle 4.43238 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.4892 (mtp) REVERT: A 248 LYS cc_start: 0.8052 (tppt) cc_final: 0.7698 (pptt) REVERT: A 349 LYS cc_start: 0.7670 (mttp) cc_final: 0.7430 (mttp) REVERT: B 130 GLU cc_start: 0.7903 (mp0) cc_final: 0.7673 (mp0) REVERT: B 336 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8850 (mt) REVERT: E 82 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7175 (mm-40) REVERT: E 98 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7299 (ttm170) REVERT: E 218 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7628 (ptp90) REVERT: R 61 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7811 (mp10) outliers start: 35 outliers final: 21 residues processed: 175 average time/residue: 0.5160 time to fit residues: 96.3971 Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 153 MET Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.194141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133068 restraints weight = 9546.646| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.55 r_work: 0.3391 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8953 Z= 0.172 Angle : 0.623 8.861 12137 Z= 0.324 Chirality : 0.044 0.210 1392 Planarity : 0.004 0.038 1528 Dihedral : 4.667 43.346 1228 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.33 % Allowed : 21.93 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.22 (0.25), residues: 1105 helix: 2.76 (0.25), residues: 384 sheet: 0.11 (0.30), residues: 295 loop : -0.47 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 27 TYR 0.020 0.002 TYR A 230 PHE 0.025 0.002 PHE E 68 TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8950) covalent geometry : angle 0.62283 (12131) SS BOND : bond 0.00384 ( 3) SS BOND : angle 0.62640 ( 6) hydrogen bonds : bond 0.03737 ( 452) hydrogen bonds : angle 4.45994 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.4910 (mtp) REVERT: A 248 LYS cc_start: 0.8019 (tppt) cc_final: 0.7675 (pptt) REVERT: B 130 GLU cc_start: 0.8037 (mp0) cc_final: 0.7795 (mp0) REVERT: B 246 ASP cc_start: 0.8586 (m-30) cc_final: 0.8308 (m-30) REVERT: B 336 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8873 (mt) REVERT: C 27 ARG cc_start: 0.5637 (OUTLIER) cc_final: 0.4837 (tpm170) REVERT: E 82 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7121 (mm-40) REVERT: E 88 SER cc_start: 0.8132 (m) cc_final: 0.7852 (t) REVERT: E 98 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7303 (ttm170) REVERT: E 218 ARG cc_start: 0.7917 (ptp90) cc_final: 0.7619 (ptp90) REVERT: R 61 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7811 (mp10) REVERT: R 219 ARG cc_start: 0.6608 (mmm-85) cc_final: 0.6248 (mtt180) REVERT: R 386 PHE cc_start: 0.6760 (m-10) cc_final: 0.6501 (m-10) outliers start: 32 outliers final: 23 residues processed: 171 average time/residue: 0.5408 time to fit residues: 98.5143 Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 153 MET Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.0170 chunk 7 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.0020 chunk 24 optimal weight: 3.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 241 ASN A 333 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.201025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145503 restraints weight = 9544.461| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.70 r_work: 0.3490 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8953 Z= 0.109 Angle : 0.582 8.916 12137 Z= 0.296 Chirality : 0.042 0.253 1392 Planarity : 0.003 0.031 1528 Dihedral : 4.274 39.032 1228 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.60 % Allowed : 22.56 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.43 (0.25), residues: 1105 helix: 2.90 (0.25), residues: 386 sheet: 0.35 (0.30), residues: 287 loop : -0.44 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 46 TYR 0.017 0.001 TYR A 230 PHE 0.014 0.001 PHE E 68 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 8950) covalent geometry : angle 0.58170 (12131) SS BOND : bond 0.00131 ( 3) SS BOND : angle 0.58763 ( 6) hydrogen bonds : bond 0.03026 ( 452) hydrogen bonds : angle 4.18647 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 158 time to evaluate : 0.276 Fit side-chains REVERT: A 349 LYS cc_start: 0.7441 (mttp) cc_final: 0.7224 (mptp) REVERT: B 130 GLU cc_start: 0.7781 (mp0) cc_final: 0.7555 (mp0) REVERT: B 336 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8869 (mt) REVERT: C 27 ARG cc_start: 0.5433 (OUTLIER) cc_final: 0.4666 (tpm170) REVERT: E 82 GLN cc_start: 0.7294 (mm-40) cc_final: 0.6862 (mm-40) REVERT: E 218 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7521 (ptp90) REVERT: R 61 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7695 (mp10) outliers start: 25 outliers final: 16 residues processed: 175 average time/residue: 0.5473 time to fit residues: 102.0651 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 374 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.191218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.132999 restraints weight = 9592.026| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.74 r_work: 0.3352 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8953 Z= 0.277 Angle : 0.725 10.189 12137 Z= 0.376 Chirality : 0.047 0.207 1392 Planarity : 0.005 0.055 1528 Dihedral : 4.918 45.782 1228 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.12 % Allowed : 22.66 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 0.99 (0.25), residues: 1105 helix: 2.48 (0.25), residues: 384 sheet: 0.22 (0.30), residues: 288 loop : -0.70 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 219 TYR 0.020 0.002 TYR A 287 PHE 0.036 0.002 PHE E 68 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 8950) covalent geometry : angle 0.72436 (12131) SS BOND : bond 0.00497 ( 3) SS BOND : angle 1.01542 ( 6) hydrogen bonds : bond 0.04452 ( 452) hydrogen bonds : angle 4.65148 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8026 (tppt) cc_final: 0.7652 (pptt) REVERT: A 349 LYS cc_start: 0.7594 (mttp) cc_final: 0.7185 (mptp) REVERT: B 246 ASP cc_start: 0.8539 (m-30) cc_final: 0.8180 (m-30) REVERT: B 336 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8872 (mt) REVERT: C 27 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5201 (tpm170) REVERT: E 82 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7087 (mm-40) REVERT: E 88 SER cc_start: 0.8136 (m) cc_final: 0.7836 (t) REVERT: E 218 ARG cc_start: 0.7923 (ptp90) cc_final: 0.7605 (ptp90) REVERT: R 61 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7780 (mp10) REVERT: R 83 MET cc_start: 0.7758 (mpp) cc_final: 0.6760 (mpp) outliers start: 30 outliers final: 21 residues processed: 181 average time/residue: 0.5400 time to fit residues: 104.0790 Evaluate side-chains 174 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 27 ARG Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 374 VAL Chi-restraints excluded: chain R residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 333 GLN R 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.196787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.136598 restraints weight = 9490.437| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.56 r_work: 0.3432 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8953 Z= 0.134 Angle : 0.616 9.064 12137 Z= 0.318 Chirality : 0.043 0.219 1392 Planarity : 0.004 0.045 1528 Dihedral : 4.651 43.212 1228 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.60 % Allowed : 24.22 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % 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: 1.21 (0.25), residues: 1105 helix: 2.73 (0.25), residues: 384 sheet: 0.20 (0.30), residues: 288 loop : -0.54 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 219 TYR 0.015 0.001 TYR A 230 PHE 0.017 0.001 PHE E 68 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8950) covalent geometry : angle 0.61562 (12131) SS BOND : bond 0.00239 ( 3) SS BOND : angle 1.02837 ( 6) hydrogen bonds : bond 0.03508 ( 452) hydrogen bonds : angle 4.36156 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.78 seconds wall clock time: 56 minutes 15.63 seconds (3375.63 seconds total)