Starting phenix.real_space_refine on Mon Mar 11 05:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_2024/7wvx_32861_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_2024/7wvx_32861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_2024/7wvx_32861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_2024/7wvx_32861_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvx_32861/03_2024/7wvx_32861_updated.pdb" } 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 Residue "R TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.30, per 1000 atoms: 0.61 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 - 3.50 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 44.0% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'R' and resid 20 through 54 removed outlier: 3.910A pdb=" N THR R 23 " --> pdb=" O ALA R 20 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU R 28 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Proline residue: R 29 - end of helix removed outlier: 3.541A pdb=" N LEU R 39 " --> pdb=" O THR R 36 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY R 43 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN R 44 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA R 51 " --> pdb=" O ILE R 48 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY R 52 " --> pdb=" O TRP R 49 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE R 53 " --> pdb=" O VAL R 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG R 54 " --> pdb=" O ALA R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 85 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 95 through 128 Processing helix chain 'R' and resid 130 through 136 Processing helix chain 'R' and resid 139 through 162 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 181 through 184 No H-bonds generated for 'chain 'R' and resid 181 through 184' Processing helix chain 'R' and resid 187 through 208 Processing helix chain 'R' and resid 211 through 231 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 Processing helix chain 'R' and resid 279 through 302 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 307 through 316 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 46 through 53 removed outlier: 3.692A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 4.666A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE A 216 " --> pdb=" O TRP A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.818A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 removed outlier: 4.234A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.432A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 24 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 30 through 43 removed outlier: 3.564A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.665A pdb=" N ILE A 265 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS A 323 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A 267 " --> pdb=" O HIS A 323 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N HIS A 196 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU A 36 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LYS A 198 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU A 38 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 200 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.914A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (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: 3.502A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, 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= D, 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= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) 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= F, 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= G, 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) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.146A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 100.30 - 107.05: 162 107.05 - 113.80: 4128 113.80 - 120.54: 2832 120.54 - 127.29: 2600 127.29 - 134.04: 77 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: 1457 2.78 - 3.31: 7004 3.31 - 3.84: 12188 3.84 - 4.37: 14514 4.37 - 4.90: 24966 Nonbonded interactions: 60129 Sorted by model distance: nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.251 2.520 nonbonded pdb=" OD1 ASP B 290 " pdb=" NH1 ARG B 314 " model vdw 2.264 2.520 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 325 " model vdw 2.280 2.440 nonbonded pdb=" O MET B 325 " pdb=" ND2 ASN B 340 " model vdw 2.300 2.520 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.324 2.520 ... (remaining 60124 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 4.050 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 22.960 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.140 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.823 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: 1.0923 time to fit residues: 152.9542 Evaluate side-chains 114 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7218 Z= 0.289 Angle : 0.574 7.683 9799 Z= 0.302 Chirality : 0.043 0.144 1154 Planarity : 0.005 0.099 1223 Dihedral : 4.499 52.292 977 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.41 % Allowed : 10.32 % Favored : 87.27 % 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: 0.61 (0.27), residues: 903 helix: 1.39 (0.25), residues: 420 sheet: 0.14 (0.39), residues: 177 loop : -0.72 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 311 PHE 0.016 0.002 PHE A 197 TYR 0.013 0.001 TYR R 221 ARG 0.004 0.001 ARG A 314 *********************** 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 141 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: R 199 THR cc_start: 0.8502 (m) cc_final: 0.8281 (m) REVERT: R 238 ARG cc_start: 0.8123 (tmt90) cc_final: 0.7877 (ttm-80) REVERT: A 33 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: A 350 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7639 (mtpt) REVERT: B 46 ARG cc_start: 0.7199 (mpp80) cc_final: 0.6971 (mtp180) outliers start: 18 outliers final: 9 residues processed: 131 average time/residue: 1.0660 time to fit residues: 147.9402 Evaluate side-chains 120 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3177 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= 0.280 Angle : 0.550 6.935 9799 Z= 0.288 Chirality : 0.042 0.144 1154 Planarity : 0.005 0.078 1223 Dihedral : 4.457 54.609 975 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.55 % Allowed : 15.55 % Favored : 81.90 % 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: 0.33 (0.27), residues: 903 helix: 1.21 (0.25), residues: 420 sheet: -0.18 (0.37), residues: 182 loop : -0.84 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.001 PHE A 197 TYR 0.008 0.001 TYR B 59 ARG 0.006 0.000 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 141 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.746 Fit side-chains REVERT: L 10 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6259 (mm) REVERT: R 199 THR cc_start: 0.8755 (m) cc_final: 0.8551 (m) REVERT: R 238 ARG cc_start: 0.8113 (tmt90) cc_final: 0.7904 (ttm-80) REVERT: A 33 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7650 (mm-30) REVERT: A 350 LYS cc_start: 0.7984 (mtmt) cc_final: 0.7702 (mtpt) outliers start: 19 outliers final: 11 residues processed: 130 average time/residue: 1.0503 time to fit residues: 145.1053 Evaluate side-chains 129 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 41 VAL 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 342 ASP Chi-restraints excluded: chain B residue 86 THR 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: 1.9990 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7218 Z= 0.252 Angle : 0.533 6.525 9799 Z= 0.281 Chirality : 0.042 0.145 1154 Planarity : 0.004 0.048 1223 Dihedral : 4.432 54.530 975 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.82 % Allowed : 17.43 % Favored : 79.76 % 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: 0.31 (0.27), residues: 903 helix: 1.15 (0.25), residues: 426 sheet: -0.27 (0.37), residues: 179 loop : -0.74 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.013 0.001 PHE A 197 TYR 0.008 0.001 TYR B 59 ARG 0.008 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 140 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.786 Fit side-chains REVERT: L 10 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6247 (mm) REVERT: R 42 LEU cc_start: 0.7980 (mt) cc_final: 0.7503 (tm) REVERT: A 33 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: A 350 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7737 (mtpt) REVERT: B 46 ARG cc_start: 0.7222 (mpp80) cc_final: 0.6998 (mtp180) outliers start: 21 outliers final: 12 residues processed: 129 average time/residue: 1.0210 time to fit residues: 140.0808 Evaluate side-chains 129 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain R residue 31 VAL Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 296 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3405 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= 0.196 Angle : 0.510 5.851 9799 Z= 0.268 Chirality : 0.041 0.142 1154 Planarity : 0.004 0.049 1223 Dihedral : 4.321 53.089 975 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.55 % Allowed : 18.77 % Favored : 78.69 % 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: 0.41 (0.27), residues: 903 helix: 1.27 (0.25), residues: 421 sheet: -0.21 (0.37), residues: 182 loop : -0.73 (0.33), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 311 PHE 0.011 0.001 PHE A 197 TYR 0.010 0.001 TYR B 124 ARG 0.007 0.000 ARG A 209 *********************** 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 139 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 0.795 Fit side-chains REVERT: R 65 LEU cc_start: 0.8107 (tt) cc_final: 0.7905 (tp) REVERT: R 113 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7941 (m) REVERT: A 33 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7590 (mm-30) REVERT: A 350 LYS cc_start: 0.8058 (mtmt) cc_final: 0.7769 (mtpt) REVERT: B 46 ARG cc_start: 0.7187 (mpp80) cc_final: 0.6963 (mtp180) outliers start: 19 outliers final: 8 residues processed: 129 average time/residue: 0.9899 time to fit residues: 136.2061 Evaluate side-chains 120 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN 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: 0.3980 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3527 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= 0.223 Angle : 0.521 6.006 9799 Z= 0.273 Chirality : 0.041 0.143 1154 Planarity : 0.004 0.049 1223 Dihedral : 4.339 52.300 975 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.95 % Allowed : 19.44 % Favored : 77.61 % 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: 0.40 (0.27), residues: 903 helix: 1.26 (0.25), residues: 423 sheet: -0.22 (0.37), residues: 182 loop : -0.75 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.002 0.001 HIS B 311 PHE 0.012 0.001 PHE A 197 TYR 0.012 0.001 TYR B 124 ARG 0.008 0.000 ARG A 209 *********************** 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 fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 0.725 Fit side-chains REVERT: R 143 MET cc_start: 0.7303 (mtt) cc_final: 0.6843 (mtt) REVERT: R 240 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7650 (mt) REVERT: A 33 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7584 (mm-30) REVERT: A 350 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7798 (mtpt) REVERT: B 46 ARG cc_start: 0.7234 (mpp80) cc_final: 0.7010 (mtp180) outliers start: 22 outliers final: 11 residues processed: 125 average time/residue: 0.9185 time to fit residues: 122.9710 Evaluate side-chains 120 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 240 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 A residue 342 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN 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: 0.5980 chunk 72 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7218 Z= 0.312 Angle : 0.573 6.551 9799 Z= 0.299 Chirality : 0.043 0.144 1154 Planarity : 0.004 0.046 1223 Dihedral : 4.596 53.011 975 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.08 % Allowed : 20.64 % 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: 0.20 (0.27), residues: 903 helix: 1.05 (0.25), residues: 428 sheet: -0.20 (0.36), residues: 185 loop : -0.90 (0.33), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.033 0.002 PHE R 37 TYR 0.011 0.001 TYR B 124 ARG 0.007 0.000 ARG A 209 *********************** 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 135 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.852 Fit side-chains REVERT: L 10 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6086 (mm) REVERT: R 240 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7674 (mt) REVERT: A 33 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: A 350 LYS cc_start: 0.8146 (mtmt) cc_final: 0.7851 (mtpt) outliers start: 23 outliers final: 13 residues processed: 125 average time/residue: 0.9530 time to fit residues: 127.2806 Evaluate side-chains 123 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 240 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 A residue 342 ASP Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET 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: 0.0170 chunk 58 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7218 Z= 0.194 Angle : 0.523 6.332 9799 Z= 0.272 Chirality : 0.041 0.141 1154 Planarity : 0.004 0.046 1223 Dihedral : 4.400 52.113 975 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.41 % Allowed : 22.25 % Favored : 75.34 % 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: 0.25 (0.27), residues: 903 helix: 1.09 (0.25), residues: 430 sheet: -0.14 (0.37), residues: 170 loop : -0.87 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.024 0.001 PHE R 37 TYR 0.014 0.001 TYR B 124 ARG 0.008 0.000 ARG A 209 *********************** 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 133 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.764 Fit side-chains REVERT: L 10 LEU cc_start: 0.6130 (OUTLIER) cc_final: 0.5849 (mm) REVERT: R 113 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7929 (m) REVERT: R 240 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7710 (mt) REVERT: A 33 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7587 (mm-30) REVERT: A 350 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7877 (mtpt) REVERT: B 290 ASP cc_start: 0.7672 (m-30) cc_final: 0.7381 (m-30) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.9143 time to fit residues: 124.7968 Evaluate side-chains 126 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 240 LEU 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 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 262 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3782 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= 0.209 Angle : 0.532 6.533 9799 Z= 0.276 Chirality : 0.041 0.142 1154 Planarity : 0.004 0.047 1223 Dihedral : 4.383 51.579 975 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.88 % Allowed : 23.32 % Favored : 74.80 % 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: 0.28 (0.27), residues: 903 helix: 1.10 (0.25), residues: 431 sheet: -0.12 (0.38), residues: 170 loop : -0.86 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.025 0.001 PHE R 37 TYR 0.016 0.001 TYR B 124 ARG 0.008 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 124 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 0.853 Fit side-chains REVERT: R 113 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7935 (m) REVERT: A 33 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7581 (mm-30) REVERT: A 209 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7808 (ttm110) REVERT: A 350 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7879 (mtpt) REVERT: B 61 MET cc_start: 0.8891 (pp-130) cc_final: 0.8403 (ppp) REVERT: B 243 THR cc_start: 0.8387 (p) cc_final: 0.8102 (p) REVERT: B 290 ASP cc_start: 0.7710 (m-30) cc_final: 0.7433 (m-30) REVERT: C 46 LYS cc_start: 0.8208 (pptt) cc_final: 0.7947 (pmtt) outliers start: 14 outliers final: 11 residues processed: 118 average time/residue: 0.9929 time to fit residues: 125.1212 Evaluate side-chains 119 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 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 A residue 352 CYS Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN 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: 2.9990 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7218 Z= 0.202 Angle : 0.527 6.370 9799 Z= 0.274 Chirality : 0.041 0.143 1154 Planarity : 0.004 0.046 1223 Dihedral : 4.344 50.853 975 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.01 % Allowed : 23.32 % Favored : 74.66 % 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: 0.33 (0.27), residues: 903 helix: 1.17 (0.25), residues: 427 sheet: -0.12 (0.38), residues: 170 loop : -0.85 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.024 0.001 PHE R 37 TYR 0.018 0.001 TYR B 124 ARG 0.008 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 122 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.877 Fit side-chains REVERT: L 10 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5728 (mm) REVERT: R 113 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7936 (m) REVERT: A 33 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: A 209 ARG cc_start: 0.8078 (ttp80) cc_final: 0.7855 (ttm110) REVERT: A 350 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7901 (mtpt) REVERT: B 61 MET cc_start: 0.8879 (pp-130) cc_final: 0.8396 (ppp) REVERT: B 243 THR cc_start: 0.8396 (p) cc_final: 0.8099 (p) REVERT: B 290 ASP cc_start: 0.7714 (m-30) cc_final: 0.7435 (m-30) REVERT: C 46 LYS cc_start: 0.8149 (pptt) cc_final: 0.7922 (pmtt) outliers start: 15 outliers final: 10 residues processed: 117 average time/residue: 1.0104 time to fit residues: 126.7875 Evaluate side-chains 117 residues out of total 786 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 104 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain R residue 41 VAL Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 191 LEU Chi-restraints excluded: chain R residue 268 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 112 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 220 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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** ** C 18 GLN ** 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 = 0.3766 r_free = 0.3766 target = 0.149428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.115606 restraints weight = 7823.768| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.83 r_work: 0.3225 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7218 Z= 0.299 Angle : 0.575 7.859 9799 Z= 0.298 Chirality : 0.043 0.147 1154 Planarity : 0.004 0.049 1223 Dihedral : 4.576 51.820 975 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.41 % Allowed : 23.86 % Favored : 73.73 % 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: 0.19 (0.27), residues: 903 helix: 1.02 (0.25), residues: 430 sheet: -0.17 (0.37), residues: 178 loop : -0.90 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.003 0.001 HIS B 311 PHE 0.025 0.002 PHE R 37 TYR 0.018 0.001 TYR B 124 ARG 0.007 0.000 ARG A 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2945.31 seconds wall clock time: 53 minutes 1.61 seconds (3181.61 seconds total)