Starting phenix.real_space_refine on Mon Jul 22 06:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x8l_38148/07_2024/8x8l_38148.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5641 2.51 5 N 1531 2.21 5 O 1620 1.98 5 H 8704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 4996 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 200 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3385 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 834 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4286 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Time building chain proxies: 8.64, per 1000 atoms: 0.49 Number of scatterers: 17555 At special positions: 0 Unit cell: (123.6, 93.936, 129.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1620 8.00 N 1531 7.00 C 5641 6.00 H 8704 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.518A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.715A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.625A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.506A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.092A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.627A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.608A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.792A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.540A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.571A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'R' and resid 43 through 67 Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 92 through 102 removed outlier: 3.578A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 143 removed outlier: 4.346A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 178 Proline residue: R 173 - end of helix Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.438A pdb=" N GLY R 183 " --> pdb=" O VAL R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 235 Processing helix chain 'R' and resid 241 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 282 through 304 removed outlier: 4.188A pdb=" N TYR R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.662A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 57 removed outlier: 6.037A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.644A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.618A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.871A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.643A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 206 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.542A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.054A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.566A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.952A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.573A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1278 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: 6.21 Time building geometry restraints manager: 15.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8678 1.02 - 1.22: 46 1.22 - 1.42: 3825 1.42 - 1.62: 5112 1.62 - 1.82: 84 Bond restraints: 17745 Sorted by residual: bond pdb=" SG CYS R 260 " pdb=" HG CYS R 260 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" ND2 ASN R 310 " pdb="HD22 ASN R 310 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" ND2 ASN R 310 " pdb="HD21 ASN R 310 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" NE ARG R 312 " pdb=" HE ARG R 312 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG A 309 " pdb=" HE ARG A 309 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 17740 not shown) Histogram of bond angle deviations from ideal: 70.11 - 82.97: 3 82.97 - 95.83: 0 95.83 - 108.68: 6039 108.68 - 121.54: 22399 121.54 - 134.40: 3463 Bond angle restraints: 31904 Sorted by residual: angle pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 70.11 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 110.00 74.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 78.81 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N VAL R 207 " pdb=" CA VAL R 207 " pdb=" C VAL R 207 " ideal model delta sigma weight residual 110.30 117.07 -6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N SER A 228 " pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 111.82 119.15 -7.33 1.16e+00 7.43e-01 3.99e+01 ... (remaining 31899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7798 17.74 - 35.49: 395 35.49 - 53.23: 168 53.23 - 70.97: 47 70.97 - 88.72: 9 Dihedral angle restraints: 8417 sinusoidal: 4475 harmonic: 3942 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -137.94 51.94 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C PHE R 211 " pdb=" N PHE R 211 " pdb=" CA PHE R 211 " pdb=" CB PHE R 211 " ideal model delta harmonic sigma weight residual -122.60 -134.21 11.61 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" CB PRO G 54 " ideal model delta harmonic sigma weight residual 115.10 124.31 -9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 8414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1299 0.095 - 0.190: 87 0.190 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA PRO G 54 " pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CB PRO G 54 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA PHE R 211 " pdb=" N PHE R 211 " pdb=" C PHE R 211 " pdb=" CB PHE R 211 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA CYS R 260 " pdb=" N CYS R 260 " pdb=" C CYS R 260 " pdb=" CB CYS R 260 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1394 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 313 " -0.112 2.00e-02 2.50e+03 1.24e-01 2.31e+02 pdb=" CD GLN R 313 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN R 313 " 0.110 2.00e-02 2.50e+03 pdb=" NE2 GLN R 313 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN R 313 " 0.184 2.00e-02 2.50e+03 pdb="HE22 GLN R 313 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 310 " -0.053 2.00e-02 2.50e+03 5.25e-02 4.14e+01 pdb=" CG ASN R 310 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN R 310 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN R 310 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN R 310 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN R 310 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 316 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" N LYS R 317 " 0.056 2.00e-02 2.50e+03 pdb=" CA LYS R 317 " -0.014 2.00e-02 2.50e+03 pdb=" H LYS R 317 " -0.024 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 35777 2.79 - 3.40: 48855 3.40 - 4.00: 63338 4.00 - 4.60: 97911 Nonbonded interactions: 246826 Sorted by model distance: nonbonded pdb=" O LYS G 19 " pdb="HD21 ASN G 23 " model vdw 1.590 1.850 nonbonded pdb="HH22 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.626 1.850 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.637 1.850 nonbonded pdb=" O ILE E 138 " pdb=" HG1 THR E 238 " model vdw 1.638 1.850 nonbonded pdb="HH12 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 1.640 1.850 ... (remaining 246821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.690 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: 0.270 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 59.050 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: 0.010 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.004 0.068 9041 Z= 0.300 Angle : 0.603 9.479 12269 Z= 0.377 Chirality : 0.050 0.476 1397 Planarity : 0.003 0.034 1557 Dihedral : 9.651 75.047 3215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 3.68 % Favored : 94.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.26), residues: 1122 helix: 2.97 (0.27), residues: 385 sheet: 1.24 (0.32), residues: 268 loop : 0.15 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 261 HIS 0.002 0.001 HIS A 329 PHE 0.015 0.001 PHE R 315 TYR 0.009 0.001 TYR R 89 ARG 0.004 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 353 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 PHE cc_start: 0.5863 (t80) cc_final: 0.5513 (t80) REVERT: R 288 PHE cc_start: 0.7375 (t80) cc_final: 0.7130 (t80) REVERT: R 315 PHE cc_start: 0.7383 (t80) cc_final: 0.7085 (t80) outliers start: 18 outliers final: 5 residues processed: 363 average time/residue: 2.3992 time to fit residues: 931.5830 Evaluate side-chains 181 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 300 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 34 HIS A 204 GLN A 213 GLN A 234 GLN B 49 GLN B 225 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN E 171 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.4518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 9041 Z= 0.274 Angle : 0.582 8.124 12269 Z= 0.308 Chirality : 0.044 0.459 1397 Planarity : 0.005 0.068 1557 Dihedral : 4.862 53.334 1249 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.15 % Allowed : 17.86 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.26), residues: 1122 helix: 2.85 (0.26), residues: 391 sheet: 0.85 (0.31), residues: 257 loop : 0.23 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 302 HIS 0.005 0.001 HIS B 230 PHE 0.014 0.002 PHE E 203 TYR 0.015 0.002 TYR R 63 ARG 0.008 0.001 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 179 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8208 (tp) cc_final: 0.7873 (mm) REVERT: B 50 MET cc_start: 0.8247 (mtm) cc_final: 0.7983 (mtm) REVERT: B 139 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7574 (ptm-80) REVERT: B 222 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6907 (pmt) REVERT: E 18 ARG cc_start: 0.7592 (tpp80) cc_final: 0.7375 (tpt-90) REVERT: R 249 MET cc_start: 0.8032 (tpp) cc_final: 0.7716 (tpp) REVERT: R 288 PHE cc_start: 0.7551 (t80) cc_final: 0.7197 (t80) REVERT: R 315 PHE cc_start: 0.7362 (t80) cc_final: 0.7054 (t80) outliers start: 49 outliers final: 19 residues processed: 211 average time/residue: 2.1704 time to fit residues: 493.7715 Evaluate side-chains 179 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 0.1980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 18 GLN B 180 GLN B 181 GLN B 264 GLN E 142 GLN R 100 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9041 Z= 0.210 Angle : 0.517 6.946 12269 Z= 0.276 Chirality : 0.043 0.435 1397 Planarity : 0.004 0.042 1557 Dihedral : 4.764 51.865 1247 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.20 % Allowed : 20.17 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.26), residues: 1122 helix: 2.90 (0.26), residues: 391 sheet: 0.66 (0.31), residues: 257 loop : 0.11 (0.31), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.004 0.001 HIS G 43 PHE 0.011 0.001 PHE B 297 TYR 0.011 0.001 TYR R 294 ARG 0.006 0.001 ARG R 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 159 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8416 (tp) cc_final: 0.8095 (mm) REVERT: B 48 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 261 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6595 (mtp85) REVERT: B 345 ASN cc_start: 0.7245 (t160) cc_final: 0.7040 (t0) REVERT: E 18 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7287 (tpt-90) REVERT: R 315 PHE cc_start: 0.7573 (t80) cc_final: 0.7239 (t80) outliers start: 40 outliers final: 20 residues processed: 187 average time/residue: 2.0179 time to fit residues: 409.2991 Evaluate side-chains 164 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 231 ASN B 18 GLN B 345 ASN E 142 GLN R 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9041 Z= 0.275 Angle : 0.557 8.221 12269 Z= 0.297 Chirality : 0.044 0.429 1397 Planarity : 0.004 0.040 1557 Dihedral : 4.771 50.597 1244 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.73 % Allowed : 18.80 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1122 helix: 2.70 (0.25), residues: 393 sheet: 0.54 (0.32), residues: 255 loop : -0.14 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 36 HIS 0.006 0.002 HIS B 230 PHE 0.013 0.002 PHE B 156 TYR 0.015 0.002 TYR R 294 ARG 0.005 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 192 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 147 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8451 (tp) cc_final: 0.8202 (mm) REVERT: B 48 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.7905 (mp) REVERT: B 50 MET cc_start: 0.8256 (mtm) cc_final: 0.7975 (mtm) REVERT: B 139 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7157 (ppt-90) REVERT: B 219 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7155 (mtt180) REVERT: B 261 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.6748 (mtp85) REVERT: E 18 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7240 (tpt-90) REVERT: E 43 LYS cc_start: 0.8495 (mppt) cc_final: 0.8262 (mmtp) REVERT: G 37 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7417 (ttp) REVERT: R 315 PHE cc_start: 0.7572 (t80) cc_final: 0.7201 (t80) outliers start: 45 outliers final: 23 residues processed: 182 average time/residue: 2.0725 time to fit residues: 408.5560 Evaluate side-chains 165 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 137 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN E 142 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9041 Z= 0.155 Angle : 0.497 6.836 12269 Z= 0.260 Chirality : 0.042 0.433 1397 Planarity : 0.004 0.039 1557 Dihedral : 4.479 48.861 1244 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.78 % Allowed : 19.85 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.26), residues: 1122 helix: 2.93 (0.26), residues: 393 sheet: 0.54 (0.32), residues: 255 loop : -0.09 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.003 0.001 HIS G 43 PHE 0.010 0.001 PHE A 189 TYR 0.010 0.001 TYR R 89 ARG 0.002 0.000 ARG A 247 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: B 38 ILE cc_start: 0.8449 (tp) cc_final: 0.8170 (mm) REVERT: B 48 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7940 (mp) REVERT: B 50 MET cc_start: 0.8264 (mtm) cc_final: 0.7996 (mtm) REVERT: B 239 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8378 (m-80) REVERT: B 261 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6746 (mtp85) REVERT: E 18 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7179 (tpt-90) REVERT: E 43 LYS cc_start: 0.8434 (mppt) cc_final: 0.8194 (mmtp) REVERT: R 249 MET cc_start: 0.7999 (tpp) cc_final: 0.7684 (tpp) REVERT: R 315 PHE cc_start: 0.7630 (t80) cc_final: 0.7267 (t80) outliers start: 36 outliers final: 22 residues processed: 179 average time/residue: 2.0120 time to fit residues: 392.2669 Evaluate side-chains 167 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 141 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 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 231 ASN B 18 GLN B 49 GLN E 142 GLN R 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9041 Z= 0.300 Angle : 0.555 9.377 12269 Z= 0.297 Chirality : 0.044 0.423 1397 Planarity : 0.004 0.043 1557 Dihedral : 4.786 48.094 1244 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.52 % Allowed : 19.75 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1122 helix: 2.52 (0.25), residues: 399 sheet: 0.48 (0.32), residues: 254 loop : -0.37 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 211 HIS 0.006 0.002 HIS B 230 PHE 0.014 0.002 PHE B 156 TYR 0.014 0.002 TYR R 294 ARG 0.006 0.001 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 141 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8515 (tp) cc_final: 0.8233 (mm) REVERT: B 48 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 139 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7187 (ppt-90) REVERT: B 219 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7252 (mtt180) REVERT: B 239 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: B 261 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.6794 (mtp85) REVERT: E 18 ARG cc_start: 0.7440 (tpp80) cc_final: 0.7192 (tpt-90) REVERT: E 43 LYS cc_start: 0.8488 (mppt) cc_final: 0.8228 (mmtp) REVERT: R 249 MET cc_start: 0.8144 (tpp) cc_final: 0.7788 (tpp) REVERT: R 315 PHE cc_start: 0.7580 (t80) cc_final: 0.7230 (t80) outliers start: 43 outliers final: 23 residues processed: 173 average time/residue: 2.0508 time to fit residues: 384.5498 Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN E 142 GLN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9041 Z= 0.139 Angle : 0.487 6.830 12269 Z= 0.255 Chirality : 0.042 0.436 1397 Planarity : 0.004 0.042 1557 Dihedral : 4.478 47.528 1244 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.94 % Allowed : 20.59 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1122 helix: 2.94 (0.26), residues: 393 sheet: 0.50 (0.32), residues: 254 loop : -0.14 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 302 HIS 0.002 0.001 HIS G 43 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR R 89 ARG 0.002 0.000 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7311 (tt0) REVERT: B 38 ILE cc_start: 0.8499 (tp) cc_final: 0.8202 (mm) REVERT: B 48 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7996 (mp) REVERT: B 49 GLN cc_start: 0.6785 (tt0) cc_final: 0.6540 (tt0) REVERT: B 239 PHE cc_start: 0.8879 (OUTLIER) cc_final: 0.8260 (m-80) REVERT: B 261 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6778 (mtp85) REVERT: E 18 ARG cc_start: 0.7435 (tpp80) cc_final: 0.7158 (tpt-90) REVERT: E 43 LYS cc_start: 0.8397 (mppt) cc_final: 0.8146 (mmtp) REVERT: R 81 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (m110) REVERT: R 249 MET cc_start: 0.8109 (tpp) cc_final: 0.7743 (tpp) REVERT: R 315 PHE cc_start: 0.7597 (t80) cc_final: 0.7217 (t80) outliers start: 28 outliers final: 17 residues processed: 170 average time/residue: 2.1273 time to fit residues: 390.9578 Evaluate side-chains 161 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 18 GLN E 142 GLN R 100 ASN R 143 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.6311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9041 Z= 0.319 Angle : 0.566 9.527 12269 Z= 0.302 Chirality : 0.044 0.427 1397 Planarity : 0.005 0.045 1557 Dihedral : 4.783 47.695 1244 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.31 % Allowed : 19.75 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1122 helix: 2.50 (0.25), residues: 399 sheet: 0.45 (0.33), residues: 254 loop : -0.41 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 211 HIS 0.008 0.002 HIS B 230 PHE 0.016 0.002 PHE R 287 TYR 0.014 0.002 TYR R 294 ARG 0.005 0.001 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: A 275 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7464 (mt) REVERT: B 38 ILE cc_start: 0.8591 (tp) cc_final: 0.8253 (mm) REVERT: B 48 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7984 (mp) REVERT: B 219 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7174 (mtt180) REVERT: B 261 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6829 (mtp85) REVERT: E 18 ARG cc_start: 0.7467 (tpp80) cc_final: 0.7201 (tpt-90) REVERT: E 43 LYS cc_start: 0.8481 (mppt) cc_final: 0.8204 (mmtp) REVERT: R 81 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8545 (m110) REVERT: R 249 MET cc_start: 0.8186 (tpp) cc_final: 0.7825 (tpp) REVERT: R 315 PHE cc_start: 0.7519 (t80) cc_final: 0.7156 (t80) outliers start: 41 outliers final: 27 residues processed: 165 average time/residue: 2.0426 time to fit residues: 365.3803 Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 274 VAL Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 49 GLN B 345 ASN R 100 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.6287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9041 Z= 0.159 Angle : 0.510 7.069 12269 Z= 0.266 Chirality : 0.042 0.434 1397 Planarity : 0.004 0.044 1557 Dihedral : 4.642 47.578 1244 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.73 % Allowed : 21.32 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1122 helix: 2.87 (0.25), residues: 393 sheet: 0.47 (0.33), residues: 254 loop : -0.21 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 211 HIS 0.003 0.001 HIS B 230 PHE 0.013 0.001 PHE R 287 TYR 0.016 0.001 TYR R 286 ARG 0.004 0.000 ARG R 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: B 38 ILE cc_start: 0.8554 (tp) cc_final: 0.8263 (mm) REVERT: B 261 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6729 (mtp85) REVERT: E 18 ARG cc_start: 0.7434 (tpp80) cc_final: 0.7159 (tpt-90) REVERT: E 43 LYS cc_start: 0.8421 (mppt) cc_final: 0.8148 (mmtp) REVERT: R 81 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8504 (m110) REVERT: R 249 MET cc_start: 0.8132 (tpp) cc_final: 0.7771 (tpp) REVERT: R 315 PHE cc_start: 0.7549 (t80) cc_final: 0.7202 (t80) outliers start: 26 outliers final: 19 residues processed: 156 average time/residue: 2.0263 time to fit residues: 343.7291 Evaluate side-chains 155 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0070 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9041 Z= 0.178 Angle : 0.523 7.365 12269 Z= 0.274 Chirality : 0.042 0.435 1397 Planarity : 0.004 0.054 1557 Dihedral : 4.600 47.905 1244 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.52 % Allowed : 21.74 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1122 helix: 2.88 (0.25), residues: 393 sheet: 0.51 (0.33), residues: 254 loop : -0.19 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.005 0.001 HIS B 230 PHE 0.015 0.001 PHE R 287 TYR 0.013 0.001 TYR R 286 ARG 0.005 0.000 ARG A 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 38 ILE cc_start: 0.8555 (tp) cc_final: 0.8260 (mm) REVERT: B 261 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7560 (mtp85) REVERT: E 18 ARG cc_start: 0.7432 (tpp80) cc_final: 0.7159 (tpt-90) REVERT: E 43 LYS cc_start: 0.8424 (mppt) cc_final: 0.8157 (mmtp) REVERT: R 81 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8505 (m110) REVERT: R 249 MET cc_start: 0.8144 (tpp) cc_final: 0.7769 (tpp) REVERT: R 315 PHE cc_start: 0.7505 (t80) cc_final: 0.7173 (t80) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 1.9881 time to fit residues: 330.8725 Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 295 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN B 18 GLN R 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102611 restraints weight = 39091.626| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.14 r_work: 0.3236 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.6541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9041 Z= 0.364 Angle : 0.604 10.270 12269 Z= 0.324 Chirality : 0.045 0.423 1397 Planarity : 0.005 0.060 1557 Dihedral : 5.049 48.649 1244 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.94 % Allowed : 21.53 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1122 helix: 2.28 (0.25), residues: 399 sheet: 0.37 (0.32), residues: 257 loop : -0.47 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 10 HIS 0.007 0.002 HIS B 230 PHE 0.018 0.002 PHE R 287 TYR 0.018 0.002 TYR R 294 ARG 0.004 0.001 ARG A 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8012.83 seconds wall clock time: 138 minutes 19.07 seconds (8299.07 seconds total)