Starting phenix.real_space_refine on Wed Feb 14 11:58:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6q_36011/02_2024/8j6q_36011_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 69 5.16 5 C 5876 2.51 5 N 1554 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "S ASP 73": "OD1" <-> "OD2" Residue "S ASP 90": "OD1" <-> "OD2" Residue "S PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9187 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "R" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2420 Classifications: {'peptide': 295} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Chain: "R" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 110 Unusual residues: {'3HR': 1, 'CLR': 2, 'IX8': 1, 'NAG': 1} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.47, per 1000 atoms: 0.60 Number of scatterers: 9187 At special positions: 0 Unit cell: (106.02, 119.04, 113.46, 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 69 16.00 O 1688 8.00 N 1554 7.00 C 5876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 266 " distance=2.03 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 405 " - " ASN R 17 " Time building additional restraints: 3.84 Conformation dependent library (CDL) restraints added in 1.9 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 14 sheets defined 34.1% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.749A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.517A pdb=" N ILE G 9 " --> pdb=" O THR G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'S' and resid 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'R' and resid 24 through 53 Proline residue: R 31 - end of helix Processing helix chain 'R' and resid 61 through 78 Processing helix chain 'R' and resid 80 through 88 Processing helix chain 'R' and resid 97 through 129 Processing helix chain 'R' and resid 135 through 138 Processing helix chain 'R' and resid 141 through 164 removed outlier: 5.087A pdb=" N HIS R 161 " --> pdb=" O GLY R 157 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU R 162 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU R 163 " --> pdb=" O THR R 159 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 173 No H-bonds generated for 'chain 'R' and resid 171 through 173' Processing helix chain 'R' and resid 188 through 217 removed outlier: 3.656A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix Processing helix chain 'R' and resid 220 through 222 No H-bonds generated for 'chain 'R' and resid 220 through 222' Processing helix chain 'R' and resid 224 through 260 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 266 through 294 removed outlier: 4.079A pdb=" N ARG R 270 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N SER R 271 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP R 290 " --> pdb=" O SER R 287 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.419A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.787A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.836A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.451A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.657A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.513A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.442A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.455A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'S' and resid 115 through 117 removed outlier: 5.958A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.220A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 226 through 231 removed outlier: 3.540A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'R' and resid 10 through 12 408 hydrogen bonds defined for protein. 1074 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: 2.71 Time building geometry restraints manager: 4.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1985 1.33 - 1.46: 2469 1.46 - 1.58: 4837 1.58 - 1.71: 1 1.71 - 1.83: 100 Bond restraints: 9392 Sorted by residual: bond pdb=" C2 IX8 R 401 " pdb=" C25 IX8 R 401 " ideal model delta sigma weight residual 1.522 1.649 -0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C4 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C2 IX8 R 401 " pdb=" N3 IX8 R 401 " ideal model delta sigma weight residual 1.451 1.538 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C15 IX8 R 401 " pdb=" C16 IX8 R 401 " ideal model delta sigma weight residual 1.460 1.545 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C11 IX8 R 401 " pdb=" N10 IX8 R 401 " ideal model delta sigma weight residual 1.359 1.442 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 9387 not shown) Histogram of bond angle deviations from ideal: 96.26 - 104.06: 103 104.06 - 111.87: 4533 111.87 - 119.67: 3481 119.67 - 127.48: 4504 127.48 - 135.29: 98 Bond angle restraints: 12719 Sorted by residual: angle pdb=" N CYS R 18 " pdb=" CA CYS R 18 " pdb=" C CYS R 18 " ideal model delta sigma weight residual 108.24 113.37 -5.13 1.32e+00 5.74e-01 1.51e+01 angle pdb=" N VAL S 64 " pdb=" CA VAL S 64 " pdb=" C VAL S 64 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 angle pdb=" C ASP S 73 " pdb=" N ASP S 74 " pdb=" CA ASP S 74 " ideal model delta sigma weight residual 120.06 124.17 -4.11 1.19e+00 7.06e-01 1.19e+01 angle pdb=" CA GLN R 170 " pdb=" CB GLN R 170 " pdb=" CG GLN R 170 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 angle pdb=" N GLU A 25 " pdb=" CA GLU A 25 " pdb=" CB GLU A 25 " ideal model delta sigma weight residual 110.28 115.52 -5.24 1.55e+00 4.16e-01 1.14e+01 ... (remaining 12714 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5174 17.82 - 35.64: 422 35.64 - 53.46: 55 53.46 - 71.28: 21 71.28 - 89.10: 6 Dihedral angle restraints: 5678 sinusoidal: 2343 harmonic: 3335 Sorted by residual: dihedral pdb=" CB CYS R 18 " pdb=" SG CYS R 18 " pdb=" SG CYS R 183 " pdb=" CB CYS R 183 " ideal model delta sinusoidal sigma weight residual 93.00 52.96 40.04 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.71 18.29 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 5675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1322 0.089 - 0.179: 101 0.179 - 0.268: 6 0.268 - 0.357: 0 0.357 - 0.446: 1 Chirality restraints: 1430 Sorted by residual: chirality pdb=" C2 IX8 R 401 " pdb=" C1 IX8 R 401 " pdb=" C25 IX8 R 401 " pdb=" N3 IX8 R 401 " both_signs ideal model delta sigma weight residual False 2.42 2.86 -0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" C3 3HR R 403 " pdb=" C2 3HR R 403 " pdb=" C4 3HR R 403 " pdb=" O2 3HR R 403 " both_signs ideal model delta sigma weight residual False -2.33 -2.58 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" C13 CLR R 402 " pdb=" C12 CLR R 402 " pdb=" C14 CLR R 402 " pdb=" C17 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.93 -2.73 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1427 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO S 75 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 38 " 0.006 2.00e-02 2.50e+03 1.36e-02 3.23e+00 pdb=" CG PHE R 38 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE R 38 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 38 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE R 38 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 38 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE R 38 " 0.001 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 537 2.73 - 3.27: 8992 3.27 - 3.82: 16297 3.82 - 4.36: 20332 4.36 - 4.90: 34029 Nonbonded interactions: 80187 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 175 " model vdw 2.191 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.206 2.440 nonbonded pdb=" OD1 ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.230 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.266 2.440 ... (remaining 80182 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: 0.560 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: 2.870 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.820 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.005 0.127 9392 Z= 0.306 Angle : 0.695 10.008 12719 Z= 0.355 Chirality : 0.048 0.446 1430 Planarity : 0.004 0.074 1595 Dihedral : 13.239 89.104 3507 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.25), residues: 1137 helix: 1.12 (0.26), residues: 384 sheet: 0.12 (0.30), residues: 283 loop : -0.23 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.028 0.002 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.005 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.2786 time to fit residues: 216.2832 Evaluate side-chains 142 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 269 ASN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9392 Z= 0.177 Angle : 0.507 8.465 12719 Z= 0.277 Chirality : 0.042 0.176 1430 Planarity : 0.004 0.066 1595 Dihedral : 6.878 89.610 1415 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.31 % Allowed : 8.94 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.25), residues: 1137 helix: 1.44 (0.26), residues: 378 sheet: 0.08 (0.30), residues: 280 loop : -0.16 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE R 277 TYR 0.024 0.001 TYR S 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 1.018 Fit side-chains REVERT: B 96 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7566 (mtt-85) REVERT: G 36 ASP cc_start: 0.8163 (m-30) cc_final: 0.7886 (m-30) REVERT: R 102 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7229 (mm) outliers start: 13 outliers final: 1 residues processed: 148 average time/residue: 1.2878 time to fit residues: 203.4189 Evaluate side-chains 144 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 141 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9392 Z= 0.226 Angle : 0.524 6.738 12719 Z= 0.283 Chirality : 0.042 0.192 1430 Planarity : 0.004 0.065 1595 Dihedral : 6.458 81.584 1415 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.25), residues: 1137 helix: 1.43 (0.27), residues: 377 sheet: 0.03 (0.29), residues: 293 loop : -0.13 (0.31), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS R 189 PHE 0.012 0.001 PHE R 277 TYR 0.025 0.001 TYR S 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.082 Fit side-chains REVERT: A 306 GLN cc_start: 0.8003 (mm110) cc_final: 0.7667 (mp10) REVERT: G 36 ASP cc_start: 0.8237 (m-30) cc_final: 0.7904 (m-30) REVERT: R 102 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7304 (mm) REVERT: R 253 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6898 (tpm170) outliers start: 12 outliers final: 5 residues processed: 141 average time/residue: 1.3366 time to fit residues: 200.8127 Evaluate side-chains 136 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 331 ASN B 268 ASN B 340 ASN R 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9392 Z= 0.242 Angle : 0.531 6.749 12719 Z= 0.286 Chirality : 0.042 0.192 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.243 73.636 1415 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.71 % Allowed : 13.47 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1137 helix: 1.43 (0.27), residues: 376 sheet: -0.03 (0.29), residues: 293 loop : -0.12 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 189 PHE 0.021 0.001 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.003 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 0.980 Fit side-chains REVERT: A 306 GLN cc_start: 0.8095 (mm110) cc_final: 0.7760 (mp10) REVERT: G 36 ASP cc_start: 0.8240 (m-30) cc_final: 0.7905 (m-30) REVERT: R 102 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7391 (mm) REVERT: R 253 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.6896 (tpm170) outliers start: 17 outliers final: 5 residues processed: 145 average time/residue: 1.3052 time to fit residues: 201.8155 Evaluate side-chains 137 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN S 186 GLN R 286 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9392 Z= 0.233 Angle : 0.526 6.668 12719 Z= 0.283 Chirality : 0.042 0.191 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.128 69.108 1415 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.71 % Allowed : 14.97 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1137 helix: 1.37 (0.27), residues: 377 sheet: -0.08 (0.29), residues: 284 loop : -0.06 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.001 PHE R 38 TYR 0.025 0.001 TYR S 190 ARG 0.006 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.192 Fit side-chains REVERT: A 306 GLN cc_start: 0.8102 (mm110) cc_final: 0.7783 (mp10) REVERT: B 259 GLN cc_start: 0.8036 (tt0) cc_final: 0.7735 (tt0) REVERT: G 36 ASP cc_start: 0.8199 (m-30) cc_final: 0.7862 (m-30) REVERT: R 102 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7444 (mm) REVERT: R 253 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6898 (tpm170) outliers start: 17 outliers final: 8 residues processed: 137 average time/residue: 1.3265 time to fit residues: 193.7658 Evaluate side-chains 133 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 123 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 222 ARG Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9392 Z= 0.223 Angle : 0.515 6.427 12719 Z= 0.277 Chirality : 0.042 0.188 1430 Planarity : 0.004 0.063 1595 Dihedral : 5.997 63.617 1415 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.91 % Allowed : 15.58 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 1137 helix: 1.43 (0.27), residues: 376 sheet: -0.11 (0.29), residues: 284 loop : -0.06 (0.30), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.025 0.001 PHE R 38 TYR 0.025 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.006 Fit side-chains REVERT: A 306 GLN cc_start: 0.8140 (mm110) cc_final: 0.7836 (mp10) REVERT: G 36 ASP cc_start: 0.8199 (m-30) cc_final: 0.7881 (m-30) REVERT: R 102 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7441 (mm) REVERT: R 253 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6893 (tpm170) outliers start: 19 outliers final: 8 residues processed: 142 average time/residue: 1.2624 time to fit residues: 191.8039 Evaluate side-chains 135 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 235 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 79 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN S 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9392 Z= 0.292 Angle : 0.563 7.437 12719 Z= 0.302 Chirality : 0.043 0.202 1430 Planarity : 0.004 0.063 1595 Dihedral : 6.106 60.808 1415 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 16.08 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1137 helix: 1.34 (0.27), residues: 376 sheet: -0.10 (0.29), residues: 294 loop : -0.10 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.029 0.002 PHE R 38 TYR 0.025 0.002 TYR S 190 ARG 0.005 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.126 Fit side-chains REVERT: A 209 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7485 (pttp) REVERT: A 306 GLN cc_start: 0.8195 (mm110) cc_final: 0.7889 (mm-40) REVERT: B 259 GLN cc_start: 0.8070 (tt0) cc_final: 0.7770 (tt0) REVERT: G 36 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: R 102 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7473 (mm) REVERT: R 253 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.6874 (tpm170) outliers start: 19 outliers final: 7 residues processed: 139 average time/residue: 1.3327 time to fit residues: 197.6483 Evaluate side-chains 139 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 84 optimal weight: 0.0980 chunk 98 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9392 Z= 0.146 Angle : 0.472 6.340 12719 Z= 0.258 Chirality : 0.041 0.156 1430 Planarity : 0.004 0.061 1595 Dihedral : 5.683 59.079 1415 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 16.98 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1137 helix: 1.55 (0.27), residues: 376 sheet: -0.11 (0.29), residues: 281 loop : -0.00 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.002 0.000 HIS S 35 PHE 0.024 0.001 PHE R 38 TYR 0.023 0.001 TYR S 190 ARG 0.006 0.000 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.057 Fit side-chains REVERT: A 4 THR cc_start: 0.7029 (t) cc_final: 0.6696 (m) REVERT: G 36 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: S 89 GLU cc_start: 0.7526 (pp20) cc_final: 0.7019 (pp20) REVERT: R 42 LEU cc_start: 0.8118 (tp) cc_final: 0.7889 (tp) REVERT: R 253 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.6898 (tpm170) outliers start: 12 outliers final: 5 residues processed: 148 average time/residue: 1.3015 time to fit residues: 205.2391 Evaluate side-chains 141 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 134 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9392 Z= 0.179 Angle : 0.496 6.363 12719 Z= 0.269 Chirality : 0.041 0.163 1430 Planarity : 0.004 0.063 1595 Dihedral : 5.677 59.753 1415 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.21 % Allowed : 17.69 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1137 helix: 1.55 (0.27), residues: 376 sheet: -0.10 (0.29), residues: 281 loop : 0.02 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.021 0.001 PHE R 38 TYR 0.021 0.001 TYR S 190 ARG 0.005 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.049 Fit side-chains REVERT: A 4 THR cc_start: 0.7013 (t) cc_final: 0.6684 (m) REVERT: G 36 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: S 89 GLU cc_start: 0.7540 (pp20) cc_final: 0.7030 (pp20) REVERT: R 42 LEU cc_start: 0.8116 (tp) cc_final: 0.7885 (tp) REVERT: R 253 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6900 (tpm170) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 1.3144 time to fit residues: 194.6972 Evaluate side-chains 138 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.0670 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9392 Z= 0.187 Angle : 0.498 6.391 12719 Z= 0.270 Chirality : 0.041 0.165 1430 Planarity : 0.004 0.062 1595 Dihedral : 5.676 59.713 1415 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.11 % Allowed : 17.89 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1137 helix: 1.54 (0.27), residues: 375 sheet: -0.10 (0.29), residues: 281 loop : -0.00 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.032 0.001 PHE R 38 TYR 0.020 0.001 TYR S 190 ARG 0.004 0.000 ARG A 208 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 1.066 Fit side-chains REVERT: A 4 THR cc_start: 0.6979 (t) cc_final: 0.6699 (m) REVERT: A 209 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7459 (pttp) REVERT: G 36 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: S 89 GLU cc_start: 0.7548 (pp20) cc_final: 0.7029 (pp20) REVERT: R 253 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6902 (tpm170) outliers start: 11 outliers final: 7 residues processed: 133 average time/residue: 1.3058 time to fit residues: 185.3496 Evaluate side-chains 138 residues out of total 995 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain R residue 159 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 253 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120054 restraints weight = 9049.764| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.98 r_work: 0.3063 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9392 Z= 0.201 Angle : 0.504 6.391 12719 Z= 0.273 Chirality : 0.042 0.167 1430 Planarity : 0.004 0.061 1595 Dihedral : 5.711 59.820 1415 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 18.09 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1137 helix: 1.51 (0.27), residues: 375 sheet: -0.12 (0.29), residues: 281 loop : -0.00 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.030 0.001 PHE R 38 TYR 0.021 0.001 TYR S 190 ARG 0.004 0.000 ARG A 208 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3888.95 seconds wall clock time: 69 minutes 54.93 seconds (4194.93 seconds total)