Starting phenix.real_space_refine on Mon Mar 11 13:08:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oya_20223/03_2024/6oya_20223_updated.pdb" } resolution = 3.3 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= -0.023 sd= 0.464 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 67 5.16 5 C 5312 2.51 5 N 1389 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 22": "OD1" <-> "OD2" Residue "A ASP 26": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 189": "OD1" <-> "OD2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 50": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N ASP 50": "OD1" <-> "OD2" Residue "N ARG 72": "NH1" <-> "NH2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "R PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 113": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "R TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 282": "OD1" <-> "OD2" Residue "R TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8321 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1655 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 495 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2612 Unusual residues: {'RET': 1} Classifications: {'peptide': 326, 'undetermined': 1} Link IDs: {'PTRANS': 18, 'TRANS': 307, None: 1} Not linked: pdbres="ASN R 326 " pdbres="RET R 401 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.62 Number of scatterers: 8321 At special positions: 0 Unit cell: (85.86, 117.66, 113.42, 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 67 16.00 O 1553 8.00 N 1389 7.00 C 5312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 32.4% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 7 through 26 removed outlier: 3.752A pdb=" N GLU A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 208 through 211 removed outlier: 3.528A pdb=" N PHE A 211 " --> pdb=" O ILE A 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.566A pdb=" N MET A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 248 " --> pdb=" O ASN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 273 removed outlier: 4.122A pdb=" N GLU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 327 through 347 removed outlier: 3.670A pdb=" N ASP A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 17 through 26 removed outlier: 4.004A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 46 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'R' and resid 15 through 17 No H-bonds generated for 'chain 'R' and resid 15 through 17' Processing helix chain 'R' and resid 28 through 30 No H-bonds generated for 'chain 'R' and resid 28 through 30' Processing helix chain 'R' and resid 34 through 63 Proline residue: R 53 - end of helix removed outlier: 4.382A pdb=" N THR R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU R 59 " --> pdb=" O ASN R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 88 Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 107 through 139 Processing helix chain 'R' and resid 150 through 168 removed outlier: 3.768A pdb=" N ILE R 154 " --> pdb=" O GLU R 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N MET R 155 " --> pdb=" O ASN R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 173 No H-bonds generated for 'chain 'R' and resid 170 through 173' Processing helix chain 'R' and resid 200 through 210 Processing helix chain 'R' and resid 213 through 234 removed outlier: 3.673A pdb=" N ALA R 233 " --> pdb=" O THR R 229 " (cutoff:3.500A) Processing helix chain 'R' and resid 243 through 262 removed outlier: 3.856A pdb=" N LYS R 248 " --> pdb=" O GLN R 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU R 249 " --> pdb=" O LYS R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 277 Processing helix chain 'R' and resid 285 through 306 removed outlier: 3.904A pdb=" N ILE R 290 " --> pdb=" O ILE R 286 " (cutoff:3.500A) Proline residue: R 291 - end of helix removed outlier: 3.615A pdb=" N SER R 298 " --> pdb=" O PHE R 294 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA R 299 " --> pdb=" O ALA R 295 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL R 300 " --> pdb=" O LYS R 296 " (cutoff:3.500A) Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing sheet with id= A, first strand: chain 'A' and resid 259 through 261 removed outlier: 4.473A pdb=" N ALA A 216 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU A 33 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 34 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL A 197 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 183 " --> pdb=" O MET A 194 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.262A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N MET B 61 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.055A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.970A 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 Processing sheet with id= E, first strand: chain 'B' and resid 220 through 223 removed outlier: 3.608A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 240 through 242 removed outlier: 3.695A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.576A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.953A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 98 removed outlier: 5.968A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 302 hydrogen bonds defined for protein. 879 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: 2.04 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2672 1.35 - 1.47: 2121 1.47 - 1.59: 3609 1.59 - 1.71: 0 1.71 - 1.84: 99 Bond restraints: 8501 Sorted by residual: bond pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.25e+00 bond pdb=" C ILE R 214 " pdb=" N PRO R 215 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.23e-02 6.61e+03 2.20e+00 bond pdb=" C ILE R 290 " pdb=" N PRO R 291 " ideal model delta sigma weight residual 1.336 1.353 -0.018 1.23e-02 6.61e+03 2.12e+00 bond pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " ideal model delta sigma weight residual 1.532 1.554 -0.022 1.56e-02 4.11e+03 2.00e+00 bond pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 1.460 1.479 -0.020 1.42e-02 4.96e+03 1.91e+00 ... (remaining 8496 not shown) Histogram of bond angle deviations from ideal: 99.96 - 106.79: 212 106.79 - 113.62: 4554 113.62 - 120.45: 3383 120.45 - 127.28: 3270 127.28 - 134.11: 83 Bond angle restraints: 11502 Sorted by residual: angle pdb=" C ASN R 310 " pdb=" N LYS R 311 " pdb=" CA LYS R 311 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" CA ASP A 189 " pdb=" CB ASP A 189 " pdb=" CG ASP A 189 " ideal model delta sigma weight residual 112.60 116.47 -3.87 1.00e+00 1.00e+00 1.50e+01 angle pdb=" N PRO R 170 " pdb=" CA PRO R 170 " pdb=" C PRO R 170 " ideal model delta sigma weight residual 110.70 115.28 -4.58 1.22e+00 6.72e-01 1.41e+01 angle pdb=" N ALA R 169 " pdb=" CA ALA R 169 " pdb=" C ALA R 169 " ideal model delta sigma weight residual 109.81 118.10 -8.29 2.21e+00 2.05e-01 1.41e+01 angle pdb=" C LEU B 126 " pdb=" N LYS B 127 " pdb=" CA LYS B 127 " ideal model delta sigma weight residual 122.82 127.91 -5.09 1.42e+00 4.96e-01 1.28e+01 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4436 17.68 - 35.36: 499 35.36 - 53.04: 74 53.04 - 70.72: 21 70.72 - 88.40: 9 Dihedral angle restraints: 5039 sinusoidal: 1986 harmonic: 3053 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 163.25 -70.25 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -132.79 46.79 1 1.00e+01 1.00e-02 3.03e+01 dihedral pdb=" CA CYS B 166 " pdb=" C CYS B 166 " pdb=" N ALA B 167 " pdb=" CA ALA B 167 " ideal model delta harmonic sigma weight residual -180.00 -156.45 -23.55 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 5036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 957 0.054 - 0.108: 247 0.108 - 0.161: 59 0.161 - 0.215: 10 0.215 - 0.269: 3 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASP A 189 " pdb=" N ASP A 189 " pdb=" C ASP A 189 " pdb=" CB ASP A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 80 " pdb=" CA ILE B 80 " pdb=" CG1 ILE B 80 " pdb=" CG2 ILE B 80 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1273 not shown) Planarity restraints: 1468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 170 " 0.062 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO R 171 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 171 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 171 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 70 " 0.044 5.00e-02 4.00e+02 6.71e-02 7.19e+00 pdb=" N PRO R 71 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 71 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO R 71 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 283 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.58e+00 pdb=" N PRO A 284 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.033 5.00e-02 4.00e+02 ... (remaining 1465 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2824 2.84 - 3.36: 7416 3.36 - 3.87: 13844 3.87 - 4.39: 15288 4.39 - 4.90: 26589 Nonbonded interactions: 65961 Sorted by model distance: nonbonded pdb=" OG1 THR A 320 " pdb=" OD2 ASP A 324 " model vdw 2.329 2.440 nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.331 2.440 nonbonded pdb=" OE1 GLU B 226 " pdb=" OH TYR N 32 " model vdw 2.341 2.440 nonbonded pdb=" O SER B 84 " pdb=" OG SER B 84 " model vdw 2.347 2.440 nonbonded pdb=" NZ LYS A 341 " pdb=" OG1 THR R 243 " model vdw 2.351 2.520 ... (remaining 65956 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: 1.170 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: 3.610 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.080 Find NCS groups from input model: 0.230 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8501 Z= 0.271 Angle : 0.877 10.956 11502 Z= 0.470 Chirality : 0.054 0.269 1276 Planarity : 0.007 0.094 1468 Dihedral : 15.281 88.402 3066 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.11 % Allowed : 10.19 % Favored : 89.70 % 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: -4.69 (0.20), residues: 1042 helix: -2.67 (0.19), residues: 369 sheet: -2.86 (0.31), residues: 206 loop : -3.55 (0.22), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.024 0.002 PHE B 151 TYR 0.025 0.002 TYR R 301 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8849 (tt0) cc_final: 0.8580 (tt0) REVERT: A 212 GLU cc_start: 0.8663 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 240 GLN cc_start: 0.9210 (tp-100) cc_final: 0.8953 (tp-100) REVERT: A 267 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7015 (ttpt) REVERT: A 302 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8825 (mm110) REVERT: A 326 GLN cc_start: 0.8268 (mm110) cc_final: 0.7871 (mm110) REVERT: A 337 ASP cc_start: 0.8694 (t0) cc_final: 0.8387 (t0) REVERT: B 125 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0) REVERT: B 264 TYR cc_start: 0.8696 (m-80) cc_final: 0.8465 (m-10) REVERT: B 289 TYR cc_start: 0.8239 (m-10) cc_final: 0.7900 (m-10) REVERT: B 308 LEU cc_start: 0.9212 (mm) cc_final: 0.8645 (mt) REVERT: B 333 ASP cc_start: 0.7945 (p0) cc_final: 0.7723 (p0) REVERT: B 337 LYS cc_start: 0.8604 (mttt) cc_final: 0.8246 (mmtm) REVERT: B 339 TRP cc_start: 0.8548 (m100) cc_final: 0.8082 (m100) REVERT: G 51 ASP cc_start: 0.7973 (t0) cc_final: 0.7268 (t70) REVERT: G 65 LYS cc_start: 0.8080 (mttt) cc_final: 0.7872 (mttm) REVERT: N 6 GLU cc_start: 0.7804 (mp0) cc_final: 0.7425 (mp0) REVERT: N 22 CYS cc_start: 0.7485 (t) cc_final: 0.7184 (t) REVERT: N 76 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8253 (mptt) REVERT: N 77 ASN cc_start: 0.7865 (t0) cc_final: 0.7376 (t0) REVERT: N 112 SER cc_start: 0.8901 (m) cc_final: 0.8679 (m) REVERT: N 123 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8281 (tp40) REVERT: R 44 MET cc_start: 0.8555 (mmp) cc_final: 0.7571 (mmm) REVERT: R 60 TYR cc_start: 0.8569 (t80) cc_final: 0.8301 (t80) REVERT: R 78 ASN cc_start: 0.9040 (t0) cc_final: 0.8721 (t0) REVERT: R 134 GLU cc_start: 0.8259 (pt0) cc_final: 0.7944 (pt0) REVERT: R 147 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: R 155 MET cc_start: 0.8488 (ttt) cc_final: 0.8274 (ttm) REVERT: R 183 MET cc_start: 0.8629 (mmm) cc_final: 0.8298 (mmt) REVERT: R 236 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8092 (mm110) REVERT: R 308 MET cc_start: 0.8655 (mmm) cc_final: 0.8046 (mmm) REVERT: R 310 ASN cc_start: 0.8921 (t0) cc_final: 0.8233 (t0) REVERT: R 317 MET cc_start: 0.8656 (mtp) cc_final: 0.8413 (mtp) outliers start: 1 outliers final: 0 residues processed: 269 average time/residue: 0.2199 time to fit residues: 78.9467 Evaluate side-chains 205 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 HIS B 6 GLN B 13 GLN B 62 HIS B 91 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN R 73 ASN R 244 GLN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8501 Z= 0.198 Angle : 0.611 8.644 11502 Z= 0.315 Chirality : 0.042 0.184 1276 Planarity : 0.004 0.048 1468 Dihedral : 5.761 70.390 1145 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.10 % Allowed : 17.28 % Favored : 80.62 % 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: -3.15 (0.23), residues: 1042 helix: -0.81 (0.25), residues: 364 sheet: -2.24 (0.34), residues: 198 loop : -3.07 (0.24), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS R 278 PHE 0.013 0.001 PHE A 330 TYR 0.022 0.002 TYR R 301 ARG 0.003 0.000 ARG G 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8823 (tt0) cc_final: 0.8587 (tt0) REVERT: A 194 MET cc_start: 0.8647 (mtt) cc_final: 0.8103 (mtp) REVERT: A 212 GLU cc_start: 0.8781 (tt0) cc_final: 0.8515 (tm-30) REVERT: A 240 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8188 (tp-100) REVERT: A 302 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8827 (mm110) REVERT: A 307 ASN cc_start: 0.8764 (t0) cc_final: 0.8560 (t0) REVERT: A 326 GLN cc_start: 0.8268 (mm110) cc_final: 0.7853 (mm110) REVERT: A 337 ASP cc_start: 0.8851 (t0) cc_final: 0.8606 (t0) REVERT: B 101 MET cc_start: 0.8750 (mmm) cc_final: 0.8471 (mmm) REVERT: B 228 ASP cc_start: 0.8567 (m-30) cc_final: 0.8199 (m-30) REVERT: B 235 PHE cc_start: 0.8839 (t80) cc_final: 0.8524 (t80) REVERT: B 261 LEU cc_start: 0.9293 (mt) cc_final: 0.8886 (mt) REVERT: B 293 ASN cc_start: 0.7763 (t0) cc_final: 0.7384 (t0) REVERT: B 308 LEU cc_start: 0.9248 (mm) cc_final: 0.8915 (mp) REVERT: B 333 ASP cc_start: 0.8094 (p0) cc_final: 0.7809 (p0) REVERT: B 337 LYS cc_start: 0.8466 (mttt) cc_final: 0.8156 (mmtm) REVERT: B 339 TRP cc_start: 0.8596 (m100) cc_final: 0.8239 (m100) REVERT: N 22 CYS cc_start: 0.7330 (t) cc_final: 0.7047 (t) REVERT: N 34 MET cc_start: 0.7764 (mmm) cc_final: 0.7480 (mmm) REVERT: N 76 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8214 (mptt) REVERT: N 77 ASN cc_start: 0.8119 (t0) cc_final: 0.7642 (t0) REVERT: N 123 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8377 (tp-100) REVERT: R 60 TYR cc_start: 0.8557 (t80) cc_final: 0.8272 (t80) REVERT: R 78 ASN cc_start: 0.9070 (t0) cc_final: 0.8706 (t0) REVERT: R 147 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8148 (mmm-85) REVERT: R 155 MET cc_start: 0.8550 (ttt) cc_final: 0.8274 (ttm) REVERT: R 183 MET cc_start: 0.8640 (mmm) cc_final: 0.8318 (tpp) REVERT: R 287 PHE cc_start: 0.8976 (t80) cc_final: 0.8726 (t80) REVERT: R 308 MET cc_start: 0.8638 (mmm) cc_final: 0.8210 (mmm) REVERT: R 310 ASN cc_start: 0.9039 (t0) cc_final: 0.8289 (t0) REVERT: R 317 MET cc_start: 0.8654 (mtp) cc_final: 0.8373 (mtp) outliers start: 19 outliers final: 11 residues processed: 238 average time/residue: 0.2048 time to fit residues: 66.8819 Evaluate side-chains 213 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 85 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8501 Z= 0.188 Angle : 0.585 8.563 11502 Z= 0.301 Chirality : 0.042 0.167 1276 Planarity : 0.004 0.044 1468 Dihedral : 5.095 54.614 1145 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.21 % Allowed : 18.38 % Favored : 78.41 % 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: -2.48 (0.25), residues: 1042 helix: -0.06 (0.27), residues: 368 sheet: -1.88 (0.36), residues: 198 loop : -2.87 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 47 HIS 0.004 0.001 HIS R 278 PHE 0.027 0.001 PHE R 293 TYR 0.019 0.001 TYR R 178 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8831 (tt0) cc_final: 0.8588 (tt0) REVERT: A 202 ASP cc_start: 0.8614 (t0) cc_final: 0.8379 (t0) REVERT: A 212 GLU cc_start: 0.8785 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 240 GLN cc_start: 0.8672 (tp-100) cc_final: 0.8209 (tp-100) REVERT: A 268 ASP cc_start: 0.6925 (m-30) cc_final: 0.6443 (p0) REVERT: A 302 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8870 (mm110) REVERT: A 312 VAL cc_start: 0.8441 (t) cc_final: 0.8156 (t) REVERT: A 326 GLN cc_start: 0.8302 (mm110) cc_final: 0.7837 (mm110) REVERT: A 337 ASP cc_start: 0.8885 (t0) cc_final: 0.8654 (t0) REVERT: A 346 ASP cc_start: 0.8835 (t0) cc_final: 0.8624 (t70) REVERT: B 228 ASP cc_start: 0.8636 (m-30) cc_final: 0.8142 (m-30) REVERT: B 235 PHE cc_start: 0.8886 (t80) cc_final: 0.8579 (t80) REVERT: B 293 ASN cc_start: 0.7808 (t0) cc_final: 0.7418 (t0) REVERT: B 308 LEU cc_start: 0.9210 (mm) cc_final: 0.8811 (mp) REVERT: B 325 MET cc_start: 0.8162 (mmt) cc_final: 0.7780 (mmt) REVERT: B 333 ASP cc_start: 0.8113 (p0) cc_final: 0.7849 (p0) REVERT: B 339 TRP cc_start: 0.8598 (m100) cc_final: 0.8331 (m100) REVERT: N 73 ASP cc_start: 0.6713 (t0) cc_final: 0.6357 (t0) REVERT: N 76 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8055 (mppt) REVERT: N 77 ASN cc_start: 0.8274 (t0) cc_final: 0.7775 (t0) REVERT: N 123 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8442 (tp-100) REVERT: R 60 TYR cc_start: 0.8547 (t80) cc_final: 0.8255 (t80) REVERT: R 78 ASN cc_start: 0.9067 (t0) cc_final: 0.8696 (t0) REVERT: R 147 ARG cc_start: 0.8403 (mmm-85) cc_final: 0.8047 (tpp80) REVERT: R 155 MET cc_start: 0.8520 (ttt) cc_final: 0.8262 (ttm) REVERT: R 183 MET cc_start: 0.8650 (mmm) cc_final: 0.8268 (tpp) REVERT: R 287 PHE cc_start: 0.9000 (t80) cc_final: 0.8751 (t80) REVERT: R 308 MET cc_start: 0.8669 (mmm) cc_final: 0.8203 (mmm) REVERT: R 310 ASN cc_start: 0.9156 (t0) cc_final: 0.8387 (t0) REVERT: R 317 MET cc_start: 0.8717 (mtp) cc_final: 0.8425 (mtp) outliers start: 29 outliers final: 23 residues processed: 221 average time/residue: 0.1872 time to fit residues: 57.1992 Evaluate side-chains 216 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 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 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8501 Z= 0.199 Angle : 0.577 8.234 11502 Z= 0.296 Chirality : 0.042 0.165 1276 Planarity : 0.003 0.043 1468 Dihedral : 4.893 56.026 1145 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.43 % Allowed : 20.27 % Favored : 75.30 % 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: -2.12 (0.26), residues: 1042 helix: 0.39 (0.28), residues: 368 sheet: -1.68 (0.36), residues: 199 loop : -2.80 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 47 HIS 0.005 0.001 HIS R 278 PHE 0.011 0.001 PHE B 151 TYR 0.018 0.001 TYR R 301 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 199 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8820 (tt0) cc_final: 0.8588 (tt0) REVERT: A 194 MET cc_start: 0.8380 (ttm) cc_final: 0.8148 (mtp) REVERT: A 202 ASP cc_start: 0.8638 (t0) cc_final: 0.8364 (t0) REVERT: A 212 GLU cc_start: 0.8831 (tt0) cc_final: 0.8520 (tm-30) REVERT: A 240 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8223 (tp-100) REVERT: A 268 ASP cc_start: 0.6933 (m-30) cc_final: 0.6593 (p0) REVERT: A 302 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8847 (mm110) REVERT: A 312 VAL cc_start: 0.8458 (t) cc_final: 0.8178 (t) REVERT: A 314 GLU cc_start: 0.7709 (pm20) cc_final: 0.7158 (pm20) REVERT: A 326 GLN cc_start: 0.8250 (mm110) cc_final: 0.7741 (mm110) REVERT: A 337 ASP cc_start: 0.8888 (t0) cc_final: 0.8642 (t0) REVERT: B 58 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8539 (pt) REVERT: B 228 ASP cc_start: 0.8602 (m-30) cc_final: 0.8080 (m-30) REVERT: B 235 PHE cc_start: 0.8922 (t80) cc_final: 0.8637 (t80) REVERT: B 293 ASN cc_start: 0.7867 (t0) cc_final: 0.7487 (t0) REVERT: B 308 LEU cc_start: 0.9194 (mm) cc_final: 0.8813 (mp) REVERT: B 333 ASP cc_start: 0.8165 (p0) cc_final: 0.7908 (p0) REVERT: B 339 TRP cc_start: 0.8634 (m100) cc_final: 0.8386 (m100) REVERT: G 46 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8117 (tp30) REVERT: N 6 GLU cc_start: 0.7673 (mp0) cc_final: 0.7049 (mm-30) REVERT: N 73 ASP cc_start: 0.6752 (t0) cc_final: 0.6367 (t0) REVERT: N 76 LYS cc_start: 0.8764 (mmmt) cc_final: 0.7971 (mppt) REVERT: N 77 ASN cc_start: 0.8334 (t0) cc_final: 0.7860 (t0) REVERT: N 123 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8479 (tp40) REVERT: R 60 TYR cc_start: 0.8530 (t80) cc_final: 0.8142 (t80) REVERT: R 78 ASN cc_start: 0.9066 (t0) cc_final: 0.8749 (t0) REVERT: R 147 ARG cc_start: 0.8412 (mmm-85) cc_final: 0.8094 (tpp80) REVERT: R 155 MET cc_start: 0.8553 (ttt) cc_final: 0.8180 (mtp) REVERT: R 183 MET cc_start: 0.8648 (mmm) cc_final: 0.8243 (tpp) REVERT: R 287 PHE cc_start: 0.9033 (t80) cc_final: 0.8776 (t80) REVERT: R 308 MET cc_start: 0.8685 (mmm) cc_final: 0.8258 (mmm) REVERT: R 310 ASN cc_start: 0.9164 (t0) cc_final: 0.8350 (t0) REVERT: R 317 MET cc_start: 0.8734 (mtp) cc_final: 0.8451 (mtp) outliers start: 40 outliers final: 25 residues processed: 227 average time/residue: 0.1841 time to fit residues: 58.5868 Evaluate side-chains 218 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8501 Z= 0.210 Angle : 0.584 7.891 11502 Z= 0.300 Chirality : 0.042 0.163 1276 Planarity : 0.003 0.039 1468 Dihedral : 4.811 55.489 1145 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.21 % Allowed : 21.48 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.26), residues: 1042 helix: 0.62 (0.28), residues: 368 sheet: -1.43 (0.38), residues: 187 loop : -2.71 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 47 HIS 0.005 0.001 HIS R 278 PHE 0.011 0.001 PHE B 253 TYR 0.018 0.001 TYR R 301 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8827 (tt0) cc_final: 0.8578 (tt0) REVERT: A 202 ASP cc_start: 0.8669 (t0) cc_final: 0.8382 (t0) REVERT: A 212 GLU cc_start: 0.8867 (tt0) cc_final: 0.8531 (tm-30) REVERT: A 240 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8208 (tp-100) REVERT: A 268 ASP cc_start: 0.6900 (m-30) cc_final: 0.6657 (p0) REVERT: A 302 GLN cc_start: 0.9254 (mm-40) cc_final: 0.8835 (mm110) REVERT: A 312 VAL cc_start: 0.8471 (t) cc_final: 0.8192 (t) REVERT: A 314 GLU cc_start: 0.7885 (pm20) cc_final: 0.7362 (pm20) REVERT: A 326 GLN cc_start: 0.8270 (mm110) cc_final: 0.7778 (mm110) REVERT: B 58 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8548 (pt) REVERT: B 235 PHE cc_start: 0.8930 (t80) cc_final: 0.8651 (t80) REVERT: B 262 MET cc_start: 0.7974 (mmm) cc_final: 0.7614 (mmt) REVERT: B 293 ASN cc_start: 0.7852 (t0) cc_final: 0.7433 (t0) REVERT: B 308 LEU cc_start: 0.9187 (mm) cc_final: 0.8858 (mp) REVERT: B 333 ASP cc_start: 0.8189 (p0) cc_final: 0.7939 (p0) REVERT: B 339 TRP cc_start: 0.8624 (m100) cc_final: 0.8369 (m100) REVERT: G 46 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8131 (tp30) REVERT: N 22 CYS cc_start: 0.7818 (t) cc_final: 0.7374 (t) REVERT: N 73 ASP cc_start: 0.6785 (t0) cc_final: 0.6543 (t0) REVERT: N 76 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8558 (mmtm) REVERT: N 77 ASN cc_start: 0.8360 (t0) cc_final: 0.7899 (t0) REVERT: N 123 GLN cc_start: 0.8945 (tp-100) cc_final: 0.8525 (tp40) REVERT: R 60 TYR cc_start: 0.8559 (t80) cc_final: 0.8057 (t80) REVERT: R 64 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: R 78 ASN cc_start: 0.9073 (t0) cc_final: 0.8763 (t0) REVERT: R 147 ARG cc_start: 0.8437 (mmm-85) cc_final: 0.8031 (tpp80) REVERT: R 155 MET cc_start: 0.8533 (ttt) cc_final: 0.8207 (mtp) REVERT: R 183 MET cc_start: 0.8642 (mmm) cc_final: 0.8222 (tpp) REVERT: R 253 MET cc_start: 0.9082 (mmm) cc_final: 0.8865 (mmm) REVERT: R 287 PHE cc_start: 0.9049 (t80) cc_final: 0.8802 (t80) REVERT: R 308 MET cc_start: 0.8680 (mmm) cc_final: 0.8236 (mmm) REVERT: R 310 ASN cc_start: 0.9182 (t0) cc_final: 0.8410 (t0) REVERT: R 317 MET cc_start: 0.8728 (mtp) cc_final: 0.8439 (mtp) outliers start: 38 outliers final: 27 residues processed: 231 average time/residue: 0.1832 time to fit residues: 59.1578 Evaluate side-chains 220 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8501 Z= 0.180 Angle : 0.588 9.513 11502 Z= 0.300 Chirality : 0.041 0.170 1276 Planarity : 0.003 0.038 1468 Dihedral : 4.779 57.680 1145 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.65 % Allowed : 22.70 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.26), residues: 1042 helix: 0.81 (0.28), residues: 367 sheet: -1.43 (0.38), residues: 193 loop : -2.57 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 47 HIS 0.011 0.001 HIS B 183 PHE 0.011 0.001 PHE B 151 TYR 0.021 0.001 TYR A 283 ARG 0.002 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8817 (tt0) cc_final: 0.8568 (tt0) REVERT: A 202 ASP cc_start: 0.8679 (t0) cc_final: 0.8399 (t0) REVERT: A 212 GLU cc_start: 0.8856 (tt0) cc_final: 0.8524 (tm-30) REVERT: A 240 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8205 (tp-100) REVERT: A 268 ASP cc_start: 0.7077 (m-30) cc_final: 0.6862 (p0) REVERT: A 302 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8829 (mm110) REVERT: A 312 VAL cc_start: 0.8440 (t) cc_final: 0.8211 (t) REVERT: A 314 GLU cc_start: 0.7842 (pm20) cc_final: 0.7405 (pm20) REVERT: A 326 GLN cc_start: 0.8277 (mm110) cc_final: 0.7792 (mm110) REVERT: A 337 ASP cc_start: 0.8841 (t0) cc_final: 0.8561 (t0) REVERT: B 58 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8517 (pt) REVERT: B 235 PHE cc_start: 0.8918 (t80) cc_final: 0.8647 (t80) REVERT: B 262 MET cc_start: 0.7974 (mmm) cc_final: 0.7609 (mmt) REVERT: B 293 ASN cc_start: 0.7861 (t0) cc_final: 0.7444 (t0) REVERT: B 308 LEU cc_start: 0.9181 (mm) cc_final: 0.8847 (mp) REVERT: B 333 ASP cc_start: 0.8173 (p0) cc_final: 0.7934 (p0) REVERT: B 339 TRP cc_start: 0.8636 (m100) cc_final: 0.8384 (m100) REVERT: G 50 GLU cc_start: 0.7800 (mp0) cc_final: 0.7575 (mp0) REVERT: N 6 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7313 (mm-30) REVERT: N 76 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8517 (tppt) REVERT: N 77 ASN cc_start: 0.8330 (t0) cc_final: 0.7843 (t0) REVERT: N 108 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8132 (m-80) REVERT: R 30 TYR cc_start: 0.7883 (p90) cc_final: 0.7540 (p90) REVERT: R 60 TYR cc_start: 0.8540 (t80) cc_final: 0.8001 (t80) REVERT: R 64 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: R 78 ASN cc_start: 0.9057 (t0) cc_final: 0.8741 (t0) REVERT: R 147 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.8033 (tpp80) REVERT: R 183 MET cc_start: 0.8634 (mmm) cc_final: 0.8195 (tpp) REVERT: R 308 MET cc_start: 0.8673 (mmm) cc_final: 0.8289 (mmm) REVERT: R 310 ASN cc_start: 0.9152 (t0) cc_final: 0.8385 (t0) REVERT: R 317 MET cc_start: 0.8731 (mtp) cc_final: 0.8441 (mtp) outliers start: 33 outliers final: 23 residues processed: 223 average time/residue: 0.1872 time to fit residues: 58.4866 Evaluate side-chains 218 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 0.0030 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8501 Z= 0.197 Angle : 0.601 8.917 11502 Z= 0.306 Chirality : 0.042 0.171 1276 Planarity : 0.003 0.037 1468 Dihedral : 4.804 53.748 1145 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.88 % Allowed : 24.03 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.26), residues: 1042 helix: 0.98 (0.28), residues: 361 sheet: -1.35 (0.38), residues: 193 loop : -2.50 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP N 47 HIS 0.004 0.001 HIS R 278 PHE 0.027 0.001 PHE R 287 TYR 0.030 0.001 TYR A 283 ARG 0.002 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8822 (tt0) cc_final: 0.8588 (tt0) REVERT: A 202 ASP cc_start: 0.8676 (t0) cc_final: 0.8391 (t0) REVERT: A 212 GLU cc_start: 0.8888 (tt0) cc_final: 0.8548 (tm-30) REVERT: A 240 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8208 (tp-100) REVERT: A 302 GLN cc_start: 0.9244 (mm-40) cc_final: 0.8819 (mm110) REVERT: A 312 VAL cc_start: 0.8432 (t) cc_final: 0.8194 (t) REVERT: A 314 GLU cc_start: 0.7849 (pm20) cc_final: 0.7371 (pm20) REVERT: A 326 GLN cc_start: 0.8304 (mm110) cc_final: 0.7821 (mm110) REVERT: A 337 ASP cc_start: 0.8844 (t0) cc_final: 0.8536 (t0) REVERT: B 57 LYS cc_start: 0.8922 (ptpp) cc_final: 0.8457 (ptmm) REVERT: B 58 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8542 (pt) REVERT: B 89 LYS cc_start: 0.8384 (mttp) cc_final: 0.8142 (mptt) REVERT: B 228 ASP cc_start: 0.8600 (m-30) cc_final: 0.8159 (m-30) REVERT: B 262 MET cc_start: 0.7964 (mmm) cc_final: 0.7579 (mmm) REVERT: B 289 TYR cc_start: 0.8206 (m-80) cc_final: 0.8002 (m-80) REVERT: B 293 ASN cc_start: 0.7922 (t0) cc_final: 0.7488 (t0) REVERT: B 308 LEU cc_start: 0.9171 (mm) cc_final: 0.8868 (mp) REVERT: B 333 ASP cc_start: 0.8200 (p0) cc_final: 0.7970 (p0) REVERT: B 339 TRP cc_start: 0.8643 (m100) cc_final: 0.8399 (m100) REVERT: G 46 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7882 (tp30) REVERT: G 50 GLU cc_start: 0.7747 (mp0) cc_final: 0.7519 (mp0) REVERT: N 76 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8350 (mppt) REVERT: N 77 ASN cc_start: 0.8227 (t0) cc_final: 0.7708 (t0) REVERT: N 108 PHE cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (m-80) REVERT: N 123 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8696 (tp-100) REVERT: R 30 TYR cc_start: 0.7816 (p90) cc_final: 0.7560 (p90) REVERT: R 60 TYR cc_start: 0.8542 (t80) cc_final: 0.7973 (t80) REVERT: R 64 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: R 78 ASN cc_start: 0.9031 (t0) cc_final: 0.8690 (t0) REVERT: R 147 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8044 (tpp80) REVERT: R 183 MET cc_start: 0.8623 (mmm) cc_final: 0.8175 (tpp) REVERT: R 308 MET cc_start: 0.8684 (mmm) cc_final: 0.8305 (mmm) REVERT: R 310 ASN cc_start: 0.9173 (t0) cc_final: 0.8409 (t0) REVERT: R 317 MET cc_start: 0.8741 (mtp) cc_final: 0.8452 (mtp) outliers start: 35 outliers final: 26 residues processed: 227 average time/residue: 0.1763 time to fit residues: 56.2444 Evaluate side-chains 220 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 59 LEU Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 GLN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8501 Z= 0.250 Angle : 0.639 9.041 11502 Z= 0.325 Chirality : 0.043 0.169 1276 Planarity : 0.003 0.038 1468 Dihedral : 4.926 51.131 1145 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.77 % Allowed : 24.36 % Favored : 71.87 % 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: -1.52 (0.27), residues: 1042 helix: 0.89 (0.28), residues: 369 sheet: -1.21 (0.38), residues: 191 loop : -2.52 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP N 47 HIS 0.006 0.001 HIS R 278 PHE 0.033 0.001 PHE R 287 TYR 0.027 0.002 TYR A 283 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8824 (tt0) cc_final: 0.8589 (tt0) REVERT: A 202 ASP cc_start: 0.8679 (t0) cc_final: 0.8402 (t0) REVERT: A 212 GLU cc_start: 0.8835 (tt0) cc_final: 0.8376 (tm-30) REVERT: A 240 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8212 (tp-100) REVERT: A 302 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8848 (mm110) REVERT: A 312 VAL cc_start: 0.8407 (t) cc_final: 0.8202 (t) REVERT: A 314 GLU cc_start: 0.7953 (pm20) cc_final: 0.7453 (pm20) REVERT: A 326 GLN cc_start: 0.8329 (mm110) cc_final: 0.7855 (mm110) REVERT: A 337 ASP cc_start: 0.8894 (t0) cc_final: 0.8589 (t0) REVERT: B 19 ARG cc_start: 0.7552 (tmt-80) cc_final: 0.6996 (ttp-110) REVERT: B 58 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8644 (pt) REVERT: B 228 ASP cc_start: 0.8632 (m-30) cc_final: 0.8166 (m-30) REVERT: B 262 MET cc_start: 0.8012 (mmm) cc_final: 0.7617 (mmm) REVERT: B 289 TYR cc_start: 0.8260 (m-80) cc_final: 0.7955 (m-80) REVERT: B 293 ASN cc_start: 0.8005 (t0) cc_final: 0.7513 (t0) REVERT: B 308 LEU cc_start: 0.9168 (mm) cc_final: 0.8871 (mp) REVERT: B 333 ASP cc_start: 0.8200 (p0) cc_final: 0.7997 (p0) REVERT: B 339 TRP cc_start: 0.8599 (m100) cc_final: 0.8371 (m100) REVERT: N 76 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8375 (mppt) REVERT: N 77 ASN cc_start: 0.8290 (t0) cc_final: 0.7751 (t0) REVERT: N 123 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8761 (tp-100) REVERT: R 30 TYR cc_start: 0.7746 (p90) cc_final: 0.7485 (p90) REVERT: R 60 TYR cc_start: 0.8539 (t80) cc_final: 0.7915 (t80) REVERT: R 64 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: R 78 ASN cc_start: 0.9075 (t0) cc_final: 0.8783 (t0) REVERT: R 147 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8070 (tpp80) REVERT: R 183 MET cc_start: 0.8630 (mmm) cc_final: 0.8168 (tpp) REVERT: R 308 MET cc_start: 0.8675 (mmm) cc_final: 0.8201 (mmm) REVERT: R 310 ASN cc_start: 0.9203 (t0) cc_final: 0.8436 (t0) REVERT: R 317 MET cc_start: 0.8752 (mtp) cc_final: 0.8464 (mtp) outliers start: 34 outliers final: 28 residues processed: 214 average time/residue: 0.1881 time to fit residues: 56.7085 Evaluate side-chains 216 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 85 PHE Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8501 Z= 0.188 Angle : 0.621 9.951 11502 Z= 0.313 Chirality : 0.042 0.169 1276 Planarity : 0.003 0.037 1468 Dihedral : 4.901 57.097 1145 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.43 % Allowed : 24.58 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.27), residues: 1042 helix: 1.02 (0.28), residues: 368 sheet: -1.21 (0.38), residues: 199 loop : -2.45 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP N 47 HIS 0.005 0.001 HIS B 183 PHE 0.032 0.001 PHE R 287 TYR 0.023 0.001 TYR A 283 ARG 0.001 0.000 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 198 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8822 (tt0) cc_final: 0.8596 (tt0) REVERT: A 202 ASP cc_start: 0.8658 (t0) cc_final: 0.8402 (t0) REVERT: A 212 GLU cc_start: 0.8809 (tt0) cc_final: 0.8406 (tm-30) REVERT: A 240 GLN cc_start: 0.8688 (tp-100) cc_final: 0.8203 (tp-100) REVERT: A 302 GLN cc_start: 0.9241 (mm-40) cc_final: 0.8824 (mm110) REVERT: A 312 VAL cc_start: 0.8446 (t) cc_final: 0.8240 (t) REVERT: A 314 GLU cc_start: 0.7930 (pm20) cc_final: 0.7459 (pm20) REVERT: A 326 GLN cc_start: 0.8339 (mm110) cc_final: 0.7873 (mm110) REVERT: A 337 ASP cc_start: 0.8845 (t0) cc_final: 0.8528 (t0) REVERT: B 15 LYS cc_start: 0.7767 (tppp) cc_final: 0.7510 (tppp) REVERT: B 19 ARG cc_start: 0.7579 (tmt-80) cc_final: 0.7032 (ttp-110) REVERT: B 58 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8603 (pt) REVERT: B 262 MET cc_start: 0.7989 (mmm) cc_final: 0.7603 (mmm) REVERT: B 289 TYR cc_start: 0.8241 (m-80) cc_final: 0.8037 (m-80) REVERT: B 293 ASN cc_start: 0.7994 (t0) cc_final: 0.7560 (t0) REVERT: B 308 LEU cc_start: 0.9159 (mm) cc_final: 0.8852 (mp) REVERT: B 339 TRP cc_start: 0.8627 (m100) cc_final: 0.8408 (m100) REVERT: N 72 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7376 (ptp-170) REVERT: N 76 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8266 (mppt) REVERT: N 77 ASN cc_start: 0.8250 (t0) cc_final: 0.7748 (t0) REVERT: N 123 GLN cc_start: 0.8983 (tp-100) cc_final: 0.8639 (tp-100) REVERT: R 30 TYR cc_start: 0.7689 (p90) cc_final: 0.7473 (p90) REVERT: R 60 TYR cc_start: 0.8532 (t80) cc_final: 0.7923 (t80) REVERT: R 64 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: R 78 ASN cc_start: 0.9035 (t0) cc_final: 0.8691 (t0) REVERT: R 147 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8054 (tpp80) REVERT: R 183 MET cc_start: 0.8618 (mmm) cc_final: 0.8143 (tpp) REVERT: R 308 MET cc_start: 0.8664 (mmm) cc_final: 0.8237 (mmm) REVERT: R 310 ASN cc_start: 0.9154 (t0) cc_final: 0.8400 (t0) REVERT: R 317 MET cc_start: 0.8758 (mtp) cc_final: 0.8472 (mtp) outliers start: 31 outliers final: 26 residues processed: 222 average time/residue: 0.1822 time to fit residues: 56.7058 Evaluate side-chains 221 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 0.0000 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 28 GLN R 244 GLN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8501 Z= 0.345 Angle : 0.706 10.366 11502 Z= 0.363 Chirality : 0.045 0.169 1276 Planarity : 0.004 0.037 1468 Dihedral : 5.172 47.877 1145 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.54 % Allowed : 24.92 % Favored : 71.54 % 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: -1.61 (0.27), residues: 1042 helix: 0.77 (0.28), residues: 373 sheet: -1.29 (0.38), residues: 202 loop : -2.57 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP N 47 HIS 0.009 0.002 HIS R 278 PHE 0.032 0.002 PHE B 235 TYR 0.024 0.002 TYR A 283 ARG 0.004 0.000 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2084 Ramachandran restraints generated. 1042 Oldfield, 0 Emsley, 1042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ASP cc_start: 0.8729 (t0) cc_final: 0.8404 (t0) REVERT: A 212 GLU cc_start: 0.8916 (tt0) cc_final: 0.8383 (tm-30) REVERT: A 240 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8230 (tp-100) REVERT: A 302 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8887 (mm110) REVERT: A 314 GLU cc_start: 0.8038 (pm20) cc_final: 0.7553 (pm20) REVERT: A 326 GLN cc_start: 0.8381 (mm110) cc_final: 0.7916 (mm110) REVERT: A 337 ASP cc_start: 0.8913 (t0) cc_final: 0.8605 (t0) REVERT: B 19 ARG cc_start: 0.7610 (tmt-80) cc_final: 0.6977 (ttp-110) REVERT: B 228 ASP cc_start: 0.8710 (m-30) cc_final: 0.8187 (m-30) REVERT: B 289 TYR cc_start: 0.8348 (m-80) cc_final: 0.7833 (m-80) REVERT: B 293 ASN cc_start: 0.7988 (t0) cc_final: 0.7415 (t0) REVERT: B 308 LEU cc_start: 0.9155 (mm) cc_final: 0.8901 (mp) REVERT: N 72 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7428 (ptp-170) REVERT: N 76 LYS cc_start: 0.8725 (mmmt) cc_final: 0.8373 (mppt) REVERT: N 77 ASN cc_start: 0.8354 (t0) cc_final: 0.7868 (t0) REVERT: N 123 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8675 (tp40) REVERT: R 60 TYR cc_start: 0.8551 (t80) cc_final: 0.8034 (t80) REVERT: R 64 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: R 78 ASN cc_start: 0.9134 (t0) cc_final: 0.8922 (t0) REVERT: R 147 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8104 (tpp80) REVERT: R 183 MET cc_start: 0.8674 (mmm) cc_final: 0.8153 (tpp) REVERT: R 308 MET cc_start: 0.8700 (mmm) cc_final: 0.8331 (mmm) REVERT: R 310 ASN cc_start: 0.9265 (t0) cc_final: 0.8481 (t0) REVERT: R 317 MET cc_start: 0.8732 (mtp) cc_final: 0.8449 (mtp) outliers start: 32 outliers final: 26 residues processed: 207 average time/residue: 0.1876 time to fit residues: 54.5713 Evaluate side-chains 208 residues out of total 904 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 53 GLN Chi-restraints excluded: chain N residue 72 ARG Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 11 VAL Chi-restraints excluded: chain R residue 17 THR Chi-restraints excluded: chain R residue 22 SER Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 64 GLN Chi-restraints excluded: chain R residue 307 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.091303 restraints weight = 16660.418| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.44 r_work: 0.3142 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8501 Z= 0.194 Angle : 0.678 11.129 11502 Z= 0.342 Chirality : 0.043 0.170 1276 Planarity : 0.003 0.038 1468 Dihedral : 5.119 58.214 1145 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.32 % Allowed : 26.14 % Favored : 70.54 % 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: -1.36 (0.27), residues: 1042 helix: 0.99 (0.28), residues: 367 sheet: -1.01 (0.38), residues: 201 loop : -2.46 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 47 HIS 0.005 0.001 HIS B 183 PHE 0.025 0.001 PHE R 287 TYR 0.021 0.002 TYR A 283 ARG 0.002 0.000 ARG B 251 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.51 seconds wall clock time: 39 minutes 33.54 seconds (2373.54 seconds total)