Starting phenix.real_space_refine on Sat Jul 26 13:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_30410_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_30410.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_30410.map" model { file = "/net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_30410_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cmu_30410/07_2025/7cmu_30410_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.56, per 1000 atoms: 0.63 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: 2.55 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.21 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: 2.99 Time building geometry restraints manager: 2.76 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: 0.440 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.820 ------------------------------------------------------------------------------- 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 : 4.13 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (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 TRP 0.005 0.000 TRP B 82 HIS 0.005 0.000 HIS B 266 PHE 0.007 0.000 PHE E 68 TYR 0.006 0.001 TYR A 230 ARG 0.003 0.000 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.17251 ( 452) hydrogen bonds : angle 6.12246 ( 1284) SS BOND : bond 0.00071 ( 3) SS BOND : angle 0.28033 ( 6) covalent geometry : bond 0.00268 ( 8950) covalent geometry : angle 0.50912 (12131) *********************** 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 : 0.990 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: 1.0099 time to fit residues: 231.6847 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 : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS B 62 HIS B 110 ASN B 220 GLN E 194 ASN R 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.205621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.147532 restraints weight = 9364.449| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.89 r_work: 0.3551 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8953 Z= 0.127 Angle : 0.549 6.588 12137 Z= 0.286 Chirality : 0.043 0.149 1392 Planarity : 0.004 0.047 1528 Dihedral : 3.988 43.850 1228 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.22 % Allowed : 11.75 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.25), residues: 1105 helix: 3.43 (0.25), residues: 392 sheet: 1.13 (0.30), residues: 273 loop : 0.41 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.018 0.001 PHE R 172 TYR 0.014 0.001 TYR E 59 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 452) hydrogen bonds : angle 4.39593 ( 1284) SS BOND : bond 0.00340 ( 3) SS BOND : angle 0.88631 ( 6) covalent geometry : bond 0.00286 ( 8950) covalent geometry : angle 0.54906 (12131) *********************** 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 192 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7487 (mtm180) cc_final: 0.6948 (mmt180) REVERT: A 248 LYS cc_start: 0.8003 (tppt) cc_final: 0.7535 (pptt) REVERT: A 269 ASN cc_start: 0.6572 (m-40) cc_final: 0.6213 (m110) REVERT: A 349 LYS cc_start: 0.7370 (mttp) cc_final: 0.7102 (mptp) REVERT: B 217 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7543 (ppp) REVERT: E 140 MET cc_start: 0.8885 (mmm) cc_final: 0.8183 (mmt) REVERT: R 113 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6890 (mmm) outliers start: 31 outliers final: 10 residues processed: 175 average time/residue: 1.1082 time to fit residues: 207.9630 Evaluate side-chains 148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 133 VAL 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 50 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 55 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 241 ASN B 44 GLN B 220 GLN B 237 ASN E 194 ASN R 65 ASN R 120 ASN R 144 GLN R 354 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.207105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.149004 restraints weight = 9518.573| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.90 r_work: 0.3561 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8953 Z= 0.102 Angle : 0.500 7.022 12137 Z= 0.259 Chirality : 0.041 0.204 1392 Planarity : 0.003 0.036 1528 Dihedral : 3.873 37.655 1228 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.01 % Allowed : 15.70 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.25), residues: 1105 helix: 3.34 (0.25), residues: 392 sheet: 0.99 (0.30), residues: 271 loop : 0.26 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.017 0.001 PHE E 68 TYR 0.011 0.001 TYR E 59 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 452) hydrogen bonds : angle 4.04903 ( 1284) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.55273 ( 6) covalent geometry : bond 0.00219 ( 8950) covalent geometry : angle 0.49962 (12131) *********************** 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 193 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.938 Fit side-chains REVERT: A 32 ARG cc_start: 0.7470 (mtm180) cc_final: 0.6996 (mmt180) REVERT: A 248 LYS cc_start: 0.7930 (tppt) cc_final: 0.7561 (pptt) REVERT: A 269 ASN cc_start: 0.6721 (m-40) cc_final: 0.6282 (m-40) REVERT: B 217 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7502 (ppp) REVERT: E 68 PHE cc_start: 0.6129 (m-80) cc_final: 0.5840 (m-80) REVERT: E 82 GLN cc_start: 0.7102 (mm-40) cc_final: 0.6817 (mm-40) REVERT: E 87 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.7055 (mpt-90) REVERT: E 192 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6212 (ptp) REVERT: E 218 ARG cc_start: 0.8010 (ptp90) cc_final: 0.7725 (ptp90) REVERT: R 324 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6690 (tm-30) REVERT: R 389 GLU cc_start: 0.7307 (mp0) cc_final: 0.7008 (pm20) outliers start: 29 outliers final: 10 residues processed: 178 average time/residue: 1.1362 time to fit residues: 216.2733 Evaluate side-chains 159 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET 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 87 ARG 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 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 133 VAL 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 0 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8300 ------------------------------------------------------------------------------- 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 241 ASN B 220 GLN B 237 ASN E 194 ASN R 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.203914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.147996 restraints weight = 9567.014| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.53 r_work: 0.3538 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8953 Z= 0.110 Angle : 0.517 7.251 12137 Z= 0.265 Chirality : 0.042 0.190 1392 Planarity : 0.003 0.030 1528 Dihedral : 3.964 37.144 1228 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.74 % Allowed : 18.09 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1105 helix: 3.30 (0.25), residues: 392 sheet: 0.83 (0.30), residues: 275 loop : 0.14 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.018 0.001 PHE E 68 TYR 0.011 0.001 TYR E 59 ARG 0.005 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 452) hydrogen bonds : angle 3.94764 ( 1284) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.44511 ( 6) covalent geometry : bond 0.00245 ( 8950) covalent geometry : angle 0.51733 (12131) *********************** 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 195 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 1.007 Fit side-chains REVERT: A 32 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7090 (mmt180) REVERT: A 248 LYS cc_start: 0.7948 (tppt) cc_final: 0.7566 (pptt) REVERT: A 287 TYR cc_start: 0.7640 (m-80) cc_final: 0.7426 (m-80) REVERT: A 309 ASP cc_start: 0.7478 (m-30) cc_final: 0.7141 (p0) REVERT: A 331 ASN cc_start: 0.7875 (m110) cc_final: 0.7488 (p0) REVERT: B 153 ASP cc_start: 0.7666 (t70) cc_final: 0.7417 (t70) REVERT: B 217 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7743 (ppp) REVERT: B 325 MET cc_start: 0.8054 (mmm) cc_final: 0.7842 (mmt) REVERT: E 68 PHE cc_start: 0.6605 (m-80) cc_final: 0.6155 (m-80) REVERT: E 82 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6935 (mm-40) REVERT: E 87 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6847 (mpt-90) REVERT: E 192 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6379 (ptp) REVERT: E 218 ARG cc_start: 0.7922 (ptp90) cc_final: 0.7680 (ptp90) REVERT: R 61 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: R 389 GLU cc_start: 0.7155 (mp0) cc_final: 0.6839 (pm20) outliers start: 36 outliers final: 15 residues processed: 177 average time/residue: 1.1651 time to fit residues: 220.1207 Evaluate side-chains 166 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER 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 87 ARG Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 61 GLN 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 153 MET 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 10 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 0.0980 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 241 ASN A 269 ASN B 220 GLN B 237 ASN E 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.204552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.146653 restraints weight = 9511.197| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.93 r_work: 0.3516 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8953 Z= 0.100 Angle : 0.506 7.457 12137 Z= 0.260 Chirality : 0.041 0.220 1392 Planarity : 0.003 0.032 1528 Dihedral : 3.888 33.964 1228 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.53 % Allowed : 18.19 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.25), residues: 1105 helix: 3.35 (0.25), residues: 392 sheet: 0.73 (0.31), residues: 275 loop : 0.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.010 0.001 TYR A 296 ARG 0.006 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 452) hydrogen bonds : angle 3.84300 ( 1284) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.53037 ( 6) covalent geometry : bond 0.00220 ( 8950) covalent geometry : angle 0.50612 (12131) *********************** 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 187 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.923 Fit side-chains REVERT: A 53 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.5180 (mpp) REVERT: A 269 ASN cc_start: 0.6700 (m-40) cc_final: 0.6476 (m110) REVERT: A 309 ASP cc_start: 0.7546 (m-30) cc_final: 0.7174 (p0) REVERT: A 331 ASN cc_start: 0.7693 (m110) cc_final: 0.7392 (p0) REVERT: B 217 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7579 (ppp) REVERT: B 325 MET cc_start: 0.7948 (mmm) cc_final: 0.7745 (mmt) REVERT: E 18 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7473 (tpp80) REVERT: E 68 PHE cc_start: 0.6675 (m-10) cc_final: 0.6175 (m-80) REVERT: E 82 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7103 (mm-40) REVERT: E 87 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6877 (mpt-90) REVERT: E 192 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6301 (ptp) REVERT: E 218 ARG cc_start: 0.7915 (ptp90) cc_final: 0.7712 (ptp90) REVERT: R 149 ARG cc_start: 0.6502 (tpt-90) cc_final: 0.4170 (ttp-110) outliers start: 34 outliers final: 16 residues processed: 172 average time/residue: 1.1786 time to fit residues: 216.4152 Evaluate side-chains 161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 185 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 217 MET 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 86 LEU Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER 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 328 THR 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 24 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 241 ASN E 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.202462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141334 restraints weight = 9438.145| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.59 r_work: 0.3499 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8953 Z= 0.120 Angle : 0.536 7.871 12137 Z= 0.277 Chirality : 0.042 0.216 1392 Planarity : 0.003 0.035 1528 Dihedral : 3.978 33.712 1228 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.37 % Allowed : 18.81 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1105 helix: 3.28 (0.25), residues: 392 sheet: 0.62 (0.30), residues: 276 loop : -0.00 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 PHE 0.015 0.001 PHE E 68 TYR 0.011 0.001 TYR E 59 ARG 0.010 0.001 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 452) hydrogen bonds : angle 3.90763 ( 1284) SS BOND : bond 0.00310 ( 3) SS BOND : angle 0.48767 ( 6) covalent geometry : bond 0.00276 ( 8950) covalent geometry : angle 0.53635 (12131) *********************** 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 194 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.996 Fit side-chains REVERT: A 53 MET cc_start: 0.5649 (OUTLIER) cc_final: 0.5078 (mpp) REVERT: A 304 GLN cc_start: 0.7971 (tt0) cc_final: 0.7749 (tt0) REVERT: A 331 ASN cc_start: 0.7821 (m110) cc_final: 0.7423 (p0) REVERT: B 214 ARG cc_start: 0.8008 (ptp-110) cc_final: 0.7655 (mtm110) REVERT: B 217 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7547 (ppp) REVERT: E 65 LYS cc_start: 0.8270 (tppt) cc_final: 0.7920 (ttmm) REVERT: E 82 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7096 (mm-40) REVERT: E 192 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6384 (ptp) REVERT: E 218 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7714 (ptp90) REVERT: R 83 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.7236 (mpp) REVERT: R 389 GLU cc_start: 0.7128 (mp0) cc_final: 0.6914 (pm20) outliers start: 42 outliers final: 25 residues processed: 174 average time/residue: 1.1188 time to fit residues: 208.1137 Evaluate side-chains 172 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 185 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 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 41 CYS 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 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 153 MET Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 328 THR 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 70 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 61 optimal weight: 0.0980 chunk 87 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 269 ASN B 237 ASN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.204763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144032 restraints weight = 9562.749| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.62 r_work: 0.3554 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8953 Z= 0.101 Angle : 0.525 8.303 12137 Z= 0.270 Chirality : 0.041 0.221 1392 Planarity : 0.003 0.033 1528 Dihedral : 3.851 33.388 1228 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.25), residues: 1105 helix: 3.41 (0.25), residues: 386 sheet: 0.54 (0.30), residues: 288 loop : 0.01 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 PHE 0.018 0.001 PHE E 68 TYR 0.010 0.001 TYR A 287 ARG 0.007 0.000 ARG E 18 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 452) hydrogen bonds : angle 3.85672 ( 1284) SS BOND : bond 0.00228 ( 3) SS BOND : angle 0.45141 ( 6) covalent geometry : bond 0.00220 ( 8950) covalent geometry : angle 0.52466 (12131) *********************** 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 175 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.959 Fit side-chains REVERT: A 53 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5016 (mpp) REVERT: A 309 ASP cc_start: 0.7585 (m-30) cc_final: 0.7303 (p0) REVERT: A 349 LYS cc_start: 0.7547 (mttp) cc_final: 0.6943 (mptp) REVERT: B 146 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (mt) REVERT: B 214 ARG cc_start: 0.8000 (ptp-110) cc_final: 0.7712 (mtm110) REVERT: B 217 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7552 (ppp) REVERT: B 325 MET cc_start: 0.7964 (mmt) cc_final: 0.7745 (mmm) REVERT: E 6 GLU cc_start: 0.7831 (mp0) cc_final: 0.7585 (mt-10) REVERT: E 65 LYS cc_start: 0.8251 (tppt) cc_final: 0.7868 (ttmm) REVERT: E 82 GLN cc_start: 0.7318 (mm-40) cc_final: 0.7005 (mm-40) REVERT: R 83 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7285 (mpp) REVERT: R 389 GLU cc_start: 0.7046 (mp0) cc_final: 0.6801 (pm20) outliers start: 29 outliers final: 21 residues processed: 162 average time/residue: 1.1300 time to fit residues: 197.4796 Evaluate side-chains 164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 185 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 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 198 LEU 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 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 83 MET Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 328 THR 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 27 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** E 194 ASN R 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.200135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.141935 restraints weight = 9558.269| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.74 r_work: 0.3467 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8953 Z= 0.142 Angle : 0.579 8.558 12137 Z= 0.299 Chirality : 0.043 0.223 1392 Planarity : 0.003 0.035 1528 Dihedral : 4.071 36.036 1228 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.95 % Allowed : 21.10 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.25), residues: 1105 helix: 3.19 (0.25), residues: 386 sheet: 0.48 (0.30), residues: 281 loop : -0.18 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.027 0.001 PHE E 68 TYR 0.012 0.001 TYR E 59 ARG 0.007 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 452) hydrogen bonds : angle 4.03475 ( 1284) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.01984 ( 6) covalent geometry : bond 0.00332 ( 8950) covalent geometry : angle 0.57874 (12131) *********************** 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 190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.5109 (mpp) REVERT: A 248 LYS cc_start: 0.7884 (tppt) cc_final: 0.7536 (pptt) REVERT: A 296 TYR cc_start: 0.7032 (t80) cc_final: 0.6507 (t80) REVERT: A 331 ASN cc_start: 0.7972 (m110) cc_final: 0.7493 (p0) REVERT: B 214 ARG cc_start: 0.8013 (ptp-110) cc_final: 0.7701 (mtm110) REVERT: B 217 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7520 (ppp) REVERT: B 325 MET cc_start: 0.7961 (mmt) cc_final: 0.7705 (mmm) REVERT: E 82 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7210 (mm-40) REVERT: E 192 MET cc_start: 0.6964 (OUTLIER) cc_final: 0.6447 (ptp) REVERT: E 218 ARG cc_start: 0.7916 (ptp90) cc_final: 0.7677 (ptp90) outliers start: 38 outliers final: 25 residues processed: 174 average time/residue: 1.1149 time to fit residues: 207.8207 Evaluate side-chains 170 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 185 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 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 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 113 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 153 MET Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 351 LEU 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 40 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 241 ASN A 294 ASN E 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.202004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143877 restraints weight = 9534.665| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.79 r_work: 0.3479 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8953 Z= 0.116 Angle : 0.558 8.540 12137 Z= 0.287 Chirality : 0.042 0.225 1392 Planarity : 0.003 0.061 1528 Dihedral : 4.037 36.128 1228 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.74 % Allowed : 22.35 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.25), residues: 1105 helix: 3.14 (0.25), residues: 386 sheet: 0.49 (0.31), residues: 280 loop : -0.23 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE E 68 TYR 0.011 0.001 TYR E 59 ARG 0.014 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 452) hydrogen bonds : angle 3.96922 ( 1284) SS BOND : bond 0.00252 ( 3) SS BOND : angle 0.40179 ( 6) covalent geometry : bond 0.00264 ( 8950) covalent geometry : angle 0.55798 (12131) *********************** 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 177 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5680 (OUTLIER) cc_final: 0.5108 (mpp) REVERT: A 296 TYR cc_start: 0.7020 (t80) cc_final: 0.6445 (t80) REVERT: B 146 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8242 (mt) REVERT: B 214 ARG cc_start: 0.8187 (ptp-110) cc_final: 0.7848 (mtm110) REVERT: B 217 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7552 (ppp) REVERT: B 325 MET cc_start: 0.7957 (mmt) cc_final: 0.7692 (mmm) REVERT: E 6 GLU cc_start: 0.7850 (mp0) cc_final: 0.7595 (mt-10) REVERT: E 18 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7648 (tpp80) REVERT: E 76 LYS cc_start: 0.7161 (mppt) cc_final: 0.6911 (ptpp) REVERT: E 82 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7044 (mm-40) REVERT: E 183 GLN cc_start: 0.7850 (tt0) cc_final: 0.7371 (tm-30) REVERT: E 218 ARG cc_start: 0.7892 (ptp90) cc_final: 0.7645 (ptp90) outliers start: 36 outliers final: 23 residues processed: 164 average time/residue: 1.1362 time to fit residues: 199.3268 Evaluate side-chains 165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 185 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 146 LEU Chi-restraints excluded: chain B residue 160 SER 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 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 E residue 71 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 130 THR Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 351 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 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 294 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.194154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.135689 restraints weight = 9581.531| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.72 r_work: 0.3385 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8953 Z= 0.241 Angle : 0.694 10.623 12137 Z= 0.357 Chirality : 0.046 0.221 1392 Planarity : 0.004 0.063 1528 Dihedral : 4.666 43.058 1228 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.74 % Allowed : 22.25 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1105 helix: 2.65 (0.25), residues: 386 sheet: 0.27 (0.30), residues: 288 loop : -0.44 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS B 91 PHE 0.017 0.002 PHE E 68 TYR 0.016 0.002 TYR E 235 ARG 0.013 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 452) hydrogen bonds : angle 4.44780 ( 1284) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.90329 ( 6) covalent geometry : bond 0.00576 ( 8950) covalent geometry : angle 0.69388 (12131) ********************** 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 191 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5202 (mpp) REVERT: A 248 LYS cc_start: 0.8042 (tppt) cc_final: 0.7720 (pptt) REVERT: B 214 ARG cc_start: 0.8083 (ptp-110) cc_final: 0.7863 (mtm110) REVERT: B 217 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7530 (ppp) REVERT: B 325 MET cc_start: 0.8007 (mmt) cc_final: 0.7734 (mmm) REVERT: E 65 LYS cc_start: 0.8334 (tppt) cc_final: 0.8022 (ttmm) REVERT: E 82 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7142 (mm-40) REVERT: E 87 ARG cc_start: 0.7352 (mpp-170) cc_final: 0.7072 (mpt-90) REVERT: E 218 ARG cc_start: 0.7961 (ptp90) cc_final: 0.7673 (ptp90) outliers start: 36 outliers final: 24 residues processed: 178 average time/residue: 1.1518 time to fit residues: 219.2433 Evaluate side-chains 176 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET 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 E residue 71 SER Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 217 SER 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 169 LEU Chi-restraints excluded: chain R residue 210 ARG Chi-restraints excluded: chain R residue 328 THR Chi-restraints excluded: chain R residue 351 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 64 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 87 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 294 ASN A 333 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139113 restraints weight = 9530.288| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.56 r_work: 0.3464 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8953 Z= 0.129 Angle : 0.606 10.038 12137 Z= 0.311 Chirality : 0.042 0.233 1392 Planarity : 0.004 0.057 1528 Dihedral : 4.455 41.265 1228 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.81 % Allowed : 23.80 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.25), residues: 1105 helix: 2.80 (0.25), residues: 386 sheet: 0.36 (0.30), residues: 287 loop : -0.38 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.033 0.001 PHE E 68 TYR 0.013 0.001 TYR E 59 ARG 0.013 0.001 ARG E 160 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 452) hydrogen bonds : angle 4.15722 ( 1284) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.03522 ( 6) covalent geometry : bond 0.00301 ( 8950) covalent geometry : angle 0.60608 (12131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7131.78 seconds wall clock time: 122 minutes 23.64 seconds (7343.64 seconds total)