Starting phenix.real_space_refine on Sat Dec 28 00:14:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.map" model { file = "/net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wvx_32861/12_2024/7wvx_32861.cif" } resolution = 2.8 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= 0.005 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 52 5.16 5 C 4554 2.51 5 N 1197 2.21 5 O 1267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7070 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 114 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2331 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 285} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1680 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2557 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 388 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 4.67, per 1000 atoms: 0.66 Number of scatterers: 7070 At special positions: 0 Unit cell: (114.95, 119.13, 85.69, 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 52 16.00 O 1267 8.00 N 1197 7.00 C 4554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 48.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'R' and resid 21 through 55 Proline residue: R 29 - end of helix removed outlier: 3.752A pdb=" N MET R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 86 removed outlier: 3.699A pdb=" N THR R 77 " --> pdb=" O SER R 73 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 94 through 129 Processing helix chain 'R' and resid 129 through 137 Processing helix chain 'R' and resid 138 through 163 removed outlier: 3.784A pdb=" N GLY R 148 " --> pdb=" O LYS R 144 " (cutoff:3.500A) Proline residue: R 149 - end of helix Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 180 through 185 removed outlier: 3.922A pdb=" N GLY R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 209 Processing helix chain 'R' and resid 210 through 232 Processing helix chain 'R' and resid 237 through 267 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 267 through 274 Processing helix chain 'R' and resid 278 through 303 removed outlier: 3.835A pdb=" N ILE R 282 " --> pdb=" O LYS R 278 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN R 285 " --> pdb=" O ASP R 281 " (cutoff:3.500A) Proline residue: R 286 - end of helix Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.799A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.118A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 217 Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.958A pdb=" N THR A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.818A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.234A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.647A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 25 removed outlier: 4.332A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.564A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192 removed outlier: 6.234A pdb=" N VAL A 34 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 4.057A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.518A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.512A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.388A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.98 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2252 1.34 - 1.46: 1339 1.46 - 1.58: 3553 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 7218 Sorted by residual: bond pdb=" SD FME L 1 " pdb=" CE FME L 1 " ideal model delta sigma weight residual 1.805 1.751 0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" CG FME L 1 " pdb=" SD FME L 1 " ideal model delta sigma weight residual 1.817 1.770 0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" N FME L 1 " pdb=" CN FME L 1 " ideal model delta sigma weight residual 1.335 1.377 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C LEU R 212 " pdb=" N PRO R 213 " ideal model delta sigma weight residual 1.336 1.350 -0.014 1.20e-02 6.94e+03 1.34e+00 bond pdb=" N FME L 1 " pdb=" CA FME L 1 " ideal model delta sigma weight residual 1.458 1.436 0.022 1.90e-02 2.77e+03 1.31e+00 ... (remaining 7213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 9645 1.56 - 3.13: 118 3.13 - 4.69: 29 4.69 - 6.25: 6 6.25 - 7.81: 1 Bond angle restraints: 9799 Sorted by residual: angle pdb=" C ASP A 329 " pdb=" N THR A 330 " pdb=" CA THR A 330 " ideal model delta sigma weight residual 122.46 125.84 -3.38 1.41e+00 5.03e-01 5.76e+00 angle pdb=" C PHE R 161 " pdb=" N LEU R 162 " pdb=" CA LEU R 162 " ideal model delta sigma weight residual 122.53 118.15 4.38 1.92e+00 2.71e-01 5.20e+00 angle pdb=" CA LEU R 162 " pdb=" CB LEU R 162 " pdb=" CG LEU R 162 " ideal model delta sigma weight residual 116.30 124.11 -7.81 3.50e+00 8.16e-02 4.98e+00 angle pdb=" CA TRP R 95 " pdb=" CB TRP R 95 " pdb=" CG TRP R 95 " ideal model delta sigma weight residual 113.60 117.82 -4.22 1.90e+00 2.77e-01 4.94e+00 angle pdb=" C PHE C 61 " pdb=" N ARG C 62 " pdb=" CA ARG C 62 " ideal model delta sigma weight residual 121.70 125.20 -3.50 1.80e+00 3.09e-01 3.78e+00 ... (remaining 9794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3894 17.28 - 34.56: 282 34.56 - 51.83: 61 51.83 - 69.11: 2 69.11 - 86.39: 2 Dihedral angle restraints: 4241 sinusoidal: 1582 harmonic: 2659 Sorted by residual: dihedral pdb=" CG ARG R 137 " pdb=" CD ARG R 137 " pdb=" NE ARG R 137 " pdb=" CZ ARG R 137 " ideal model delta sinusoidal sigma weight residual 90.00 134.63 -44.63 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " pdb=" CZ ARG B 22 " ideal model delta sinusoidal sigma weight residual 180.00 -137.47 -42.53 2 1.50e+01 4.44e-03 9.75e+00 dihedral pdb=" CA LYS C 14 " pdb=" CB LYS C 14 " pdb=" CG LYS C 14 " pdb=" CD LYS C 14 " ideal model delta sinusoidal sigma weight residual -60.00 -116.00 56.00 3 1.50e+01 4.44e-03 9.38e+00 ... (remaining 4238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 719 0.029 - 0.058: 263 0.058 - 0.087: 112 0.087 - 0.115: 53 0.115 - 0.144: 7 Chirality restraints: 1154 Sorted by residual: chirality pdb=" CB ILE R 101 " pdb=" CA ILE R 101 " pdb=" CG1 ILE R 101 " pdb=" CG2 ILE R 101 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" CA ILE B 81 " pdb=" N ILE B 81 " pdb=" C ILE B 81 " pdb=" CB ILE B 81 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO R 187 " pdb=" N PRO R 187 " pdb=" C PRO R 187 " pdb=" CB PRO R 187 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1151 not shown) Planarity restraints: 1223 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 148 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.08e+00 pdb=" N PRO R 149 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 149 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 149 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 186 " 0.032 5.00e-02 4.00e+02 4.89e-02 3.83e+00 pdb=" N PRO R 187 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO R 187 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 187 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO B 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 ... (remaining 1220 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1451 2.78 - 3.31: 6959 3.31 - 3.84: 12150 3.84 - 4.37: 14439 4.37 - 4.90: 24954 Nonbonded interactions: 59953 Sorted by model distance: nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.251 3.120 nonbonded pdb=" OD1 ASP B 290 " pdb=" NH1 ARG B 314 " model vdw 2.264 3.120 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.280 3.040 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.300 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.324 3.120 ... (remaining 59948 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: 0.950 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.000 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.002 0.054 7218 Z= 0.134 Angle : 0.492 7.814 9799 Z= 0.267 Chirality : 0.040 0.144 1154 Planarity : 0.004 0.051 1223 Dihedral : 12.148 86.390 2512 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.28), residues: 903 helix: 1.86 (0.25), residues: 407 sheet: 0.42 (0.42), residues: 158 loop : -0.95 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 95 HIS 0.002 0.000 HIS B 183 PHE 0.009 0.001 PHE B 199 TYR 0.005 0.001 TYR A 231 ARG 0.004 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.934 Fit side-chains REVERT: R 65 LEU cc_start: 0.8050 (tt) cc_final: 0.7831 (tm) REVERT: A 194 ASP cc_start: 0.7448 (m-30) cc_final: 0.7237 (m-30) outliers start: 0 outliers final: 1 residues processed: 132 average time/residue: 1.1571 time to fit residues: 161.8331 Evaluate side-chains 114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 129 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 HIS ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7218 Z= 0.250 Angle : 0.565 7.714 9799 Z= 0.297 Chirality : 0.043 0.143 1154 Planarity : 0.005 0.098 1223 Dihedral : 4.262 45.405 977 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.01 % Allowed : 10.46 % Favored : 87.53 % 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: 0.84 (0.28), residues: 903 helix: 1.75 (0.25), residues: 422 sheet: -0.03 (0.37), residues: 189 loop : -0.73 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.014 0.002 PHE A 197 TYR 0.011 0.001 TYR R 221 ARG 0.005 0.001 ARG R 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.847 Fit side-chains REVERT: R 65 LEU cc_start: 0.8257 (tt) cc_final: 0.7967 (tm) REVERT: R 199 THR cc_start: 0.8382 (m) cc_final: 0.8156 (m) REVERT: R 238 ARG cc_start: 0.8083 (tmt90) cc_final: 0.7883 (tpt-90) REVERT: R 304 PHE cc_start: 0.8130 (m-10) cc_final: 0.7921 (m-10) REVERT: A 33 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 194 ASP cc_start: 0.7592 (m-30) cc_final: 0.7374 (m-30) REVERT: A 314 ARG cc_start: 0.7863 (mmt-90) cc_final: 0.7476 (mmt90) REVERT: A 350 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7701 (mtpt) REVERT: B 220 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7417 (mt0) REVERT: C 21 MET cc_start: 0.4004 (OUTLIER) cc_final: 0.3181 (ppp) outliers start: 15 outliers final: 7 residues processed: 135 average time/residue: 1.1850 time to fit residues: 169.3697 Evaluate side-chains 126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 174 THR Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain C residue 21 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 72 optimal weight: 0.1980 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7218 Z= 0.212 Angle : 0.541 9.350 9799 Z= 0.281 Chirality : 0.042 0.145 1154 Planarity : 0.004 0.058 1223 Dihedral : 4.092 42.135 975 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 15.55 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.28), residues: 903 helix: 1.64 (0.25), residues: 425 sheet: 0.04 (0.38), residues: 176 loop : -0.74 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 62 PHE 0.011 0.001 PHE A 197 TYR 0.007 0.001 TYR R 221 ARG 0.006 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.953 Fit side-chains REVERT: R 199 THR cc_start: 0.8531 (m) cc_final: 0.8310 (m) REVERT: A 33 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (mm-30) REVERT: A 194 ASP cc_start: 0.7562 (m-30) cc_final: 0.7335 (m-30) REVERT: A 209 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7935 (ttm110) REVERT: A 350 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7822 (mtpt) REVERT: B 45 MET cc_start: 0.8095 (mtt) cc_final: 0.7743 (mtt) REVERT: B 52 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7925 (mtp85) REVERT: B 220 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7553 (mt0) outliers start: 15 outliers final: 4 residues processed: 132 average time/residue: 1.2586 time to fit residues: 175.2756 Evaluate side-chains 118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 220 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 0.1980 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 294 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7218 Z= 0.197 Angle : 0.526 7.977 9799 Z= 0.275 Chirality : 0.041 0.144 1154 Planarity : 0.004 0.048 1223 Dihedral : 4.043 41.724 975 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.14 % Allowed : 17.16 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 903 helix: 1.75 (0.25), residues: 419 sheet: -0.31 (0.37), residues: 182 loop : -0.66 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.019 0.001 PHE R 37 TYR 0.007 0.001 TYR B 124 ARG 0.005 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.872 Fit side-chains REVERT: R 199 THR cc_start: 0.8575 (m) cc_final: 0.8355 (m) REVERT: R 238 ARG cc_start: 0.8243 (tpt-90) cc_final: 0.7988 (tpt-90) REVERT: A 33 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7625 (mm-30) REVERT: A 194 ASP cc_start: 0.7610 (m-30) cc_final: 0.7370 (m-30) REVERT: A 314 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7485 (mmt90) REVERT: A 350 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7825 (mtpt) REVERT: B 45 MET cc_start: 0.8067 (mtt) cc_final: 0.7765 (mtt) REVERT: B 52 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7864 (mtp85) REVERT: B 220 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7369 (mt0) outliers start: 16 outliers final: 8 residues processed: 126 average time/residue: 1.1686 time to fit residues: 155.8837 Evaluate side-chains 122 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 220 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 0.1980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7218 Z= 0.175 Angle : 0.515 8.302 9799 Z= 0.267 Chirality : 0.041 0.144 1154 Planarity : 0.004 0.049 1223 Dihedral : 3.992 40.782 975 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.82 % Allowed : 17.96 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 903 helix: 1.76 (0.25), residues: 420 sheet: -0.25 (0.36), residues: 187 loop : -0.72 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS C 44 PHE 0.012 0.001 PHE R 37 TYR 0.012 0.001 TYR B 124 ARG 0.004 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.866 Fit side-chains REVERT: R 238 ARG cc_start: 0.8194 (tpt-90) cc_final: 0.7919 (tpt-90) REVERT: A 33 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7604 (mm-30) REVERT: A 194 ASP cc_start: 0.7538 (m-30) cc_final: 0.7305 (m-30) REVERT: A 314 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.7481 (mmt90) REVERT: A 350 LYS cc_start: 0.8124 (mtmt) cc_final: 0.7814 (mtpt) REVERT: B 46 ARG cc_start: 0.7135 (mpp80) cc_final: 0.6921 (mtp180) REVERT: B 220 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7390 (mt0) REVERT: B 243 THR cc_start: 0.8313 (p) cc_final: 0.8023 (p) outliers start: 21 outliers final: 10 residues processed: 134 average time/residue: 1.1557 time to fit residues: 164.3271 Evaluate side-chains 123 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 0.3980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7218 Z= 0.235 Angle : 0.538 8.629 9799 Z= 0.280 Chirality : 0.042 0.149 1154 Planarity : 0.004 0.048 1223 Dihedral : 3.968 25.819 975 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.68 % Allowed : 19.44 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.28), residues: 903 helix: 1.70 (0.25), residues: 420 sheet: -0.50 (0.36), residues: 182 loop : -0.72 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.012 0.001 PHE A 197 TYR 0.014 0.001 TYR B 124 ARG 0.004 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.823 Fit side-chains REVERT: R 42 LEU cc_start: 0.8185 (mp) cc_final: 0.7666 (tm) REVERT: R 238 ARG cc_start: 0.8202 (tpt-90) cc_final: 0.7917 (tpt-90) REVERT: A 33 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 314 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7560 (mmt90) REVERT: A 350 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7763 (mtpt) REVERT: B 46 ARG cc_start: 0.7129 (mpp80) cc_final: 0.6901 (mtp180) REVERT: B 220 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7448 (mt0) outliers start: 20 outliers final: 11 residues processed: 129 average time/residue: 1.1050 time to fit residues: 151.6824 Evaluate side-chains 126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7218 Z= 0.258 Angle : 0.558 8.383 9799 Z= 0.289 Chirality : 0.042 0.148 1154 Planarity : 0.004 0.048 1223 Dihedral : 4.072 27.682 975 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.82 % Allowed : 19.97 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 903 helix: 1.69 (0.25), residues: 419 sheet: -0.57 (0.35), residues: 181 loop : -0.73 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS B 311 PHE 0.013 0.001 PHE A 197 TYR 0.014 0.001 TYR B 124 ARG 0.003 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.802 Fit side-chains REVERT: R 42 LEU cc_start: 0.8204 (mp) cc_final: 0.7680 (tm) REVERT: R 238 ARG cc_start: 0.8246 (tpt-90) cc_final: 0.7936 (tpt-90) REVERT: A 33 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7614 (mm-30) REVERT: A 314 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7582 (mmt90) REVERT: A 350 LYS cc_start: 0.8283 (mtmt) cc_final: 0.7982 (mtpt) REVERT: B 46 ARG cc_start: 0.7162 (mpp80) cc_final: 0.6944 (mtp180) outliers start: 21 outliers final: 10 residues processed: 124 average time/residue: 1.0819 time to fit residues: 142.7720 Evaluate side-chains 121 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 297 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7218 Z= 0.203 Angle : 0.538 7.958 9799 Z= 0.280 Chirality : 0.041 0.146 1154 Planarity : 0.004 0.049 1223 Dihedral : 4.029 25.499 975 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.01 % Allowed : 21.58 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.27), residues: 903 helix: 1.73 (0.25), residues: 418 sheet: -0.54 (0.35), residues: 182 loop : -0.80 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE A 197 TYR 0.013 0.001 TYR B 124 ARG 0.003 0.000 ARG R 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.826 Fit side-chains REVERT: R 42 LEU cc_start: 0.8222 (mp) cc_final: 0.7705 (tm) REVERT: R 143 MET cc_start: 0.7260 (mtt) cc_final: 0.6900 (mtt) REVERT: R 238 ARG cc_start: 0.8232 (tpt-90) cc_final: 0.7925 (tpt-90) REVERT: A 33 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: A 314 ARG cc_start: 0.7829 (mmt-90) cc_final: 0.7418 (mmt90) REVERT: A 350 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8034 (mtpt) REVERT: B 46 ARG cc_start: 0.7188 (mpp80) cc_final: 0.6986 (mtp180) outliers start: 15 outliers final: 9 residues processed: 123 average time/residue: 1.0895 time to fit residues: 142.7999 Evaluate side-chains 119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.0270 chunk 62 optimal weight: 0.0270 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 0.0000 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.3300 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7218 Z= 0.166 Angle : 0.525 7.801 9799 Z= 0.272 Chirality : 0.041 0.141 1154 Planarity : 0.004 0.049 1223 Dihedral : 3.915 22.523 975 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.47 % Allowed : 21.98 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 903 helix: 1.76 (0.25), residues: 422 sheet: -0.46 (0.36), residues: 180 loop : -0.74 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.000 HIS B 311 PHE 0.008 0.001 PHE R 37 TYR 0.013 0.001 TYR B 124 ARG 0.006 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.811 Fit side-chains REVERT: R 42 LEU cc_start: 0.8178 (mp) cc_final: 0.7660 (tm) REVERT: R 238 ARG cc_start: 0.8231 (tpt-90) cc_final: 0.7941 (tpt-90) REVERT: A 194 ASP cc_start: 0.7593 (m-30) cc_final: 0.7331 (m-30) REVERT: A 314 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7401 (mmt90) REVERT: A 350 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7996 (mtpt) outliers start: 11 outliers final: 8 residues processed: 123 average time/residue: 0.9491 time to fit residues: 124.7764 Evaluate side-chains 115 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 7 optimal weight: 0.3980 chunk 54 optimal weight: 0.0050 chunk 43 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7218 Z= 0.174 Angle : 0.534 7.744 9799 Z= 0.277 Chirality : 0.041 0.143 1154 Planarity : 0.004 0.049 1223 Dihedral : 3.880 21.825 975 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.47 % Allowed : 22.25 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.28), residues: 903 helix: 1.73 (0.25), residues: 423 sheet: -0.40 (0.36), residues: 181 loop : -0.74 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.024 0.001 PHE R 37 TYR 0.015 0.001 TYR B 124 ARG 0.006 0.000 ARG A 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1806 Ramachandran restraints generated. 903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.852 Fit side-chains REVERT: R 238 ARG cc_start: 0.8223 (tpt-90) cc_final: 0.7938 (tpt-90) REVERT: A 194 ASP cc_start: 0.7586 (m-30) cc_final: 0.7331 (m-30) REVERT: A 314 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7414 (mmt90) outliers start: 11 outliers final: 10 residues processed: 117 average time/residue: 1.0393 time to fit residues: 129.6286 Evaluate side-chains 113 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 268 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106725 restraints weight = 7902.733| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.88 r_work: 0.3093 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 7218 Z= 0.418 Angle : 0.660 8.192 9799 Z= 0.344 Chirality : 0.046 0.154 1154 Planarity : 0.005 0.061 1223 Dihedral : 4.561 34.121 975 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.47 % Allowed : 22.12 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.27), residues: 903 helix: 1.47 (0.25), residues: 419 sheet: -0.65 (0.35), residues: 190 loop : -0.99 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.022 0.002 PHE R 37 TYR 0.016 0.002 TYR B 124 ARG 0.006 0.001 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.70 seconds wall clock time: 55 minutes 56.43 seconds (3356.43 seconds total)