Starting phenix.real_space_refine on Sat Apr 6 22:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jso_36625/04_2024/8jso_36625_updated.pdb" } resolution = 3.4 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= -0.001 sd= 0.031 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 68 5.16 5 C 5764 2.51 5 N 1546 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "S PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9045 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2292 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1777 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'1WE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.57 Number of scatterers: 9045 At special positions: 0 Unit cell: (113.9, 130.05, 111.35, 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 68 16.00 O 1667 8.00 N 1546 7.00 C 5764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB 1WE R 401 " Number of C-beta restraints generated: 2148 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 34.1% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 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 233 through 243 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 317 Processing helix chain 'A' and resid 339 through 357 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.557A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'R' and resid 93 through 125 removed outlier: 3.973A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA R 124 " --> pdb=" O ASP R 120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 125 " --> pdb=" O ARG R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 130 No H-bonds generated for 'chain 'R' and resid 128 through 130' Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix removed outlier: 4.256A pdb=" N MET R 158 " --> pdb=" O PHE R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 177 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 201 through 227 removed outlier: 4.116A pdb=" N ILE R 205 " --> pdb=" O ILE R 201 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N MET R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 276 removed outlier: 4.058A pdb=" N VAL R 259 " --> pdb=" O ILE R 255 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 318 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 221 through 223 No H-bonds generated for 'chain 'S' and resid 221 through 223' Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.866A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 43 Processing sheet with id= A, first strand: chain 'A' and resid 34 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 226 removed outlier: 7.276A pdb=" N SER A 253 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 223 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 255 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL A 225 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 257 " --> pdb=" O VAL A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.153A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.518A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.594A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.637A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.597A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.956A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.797A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN S 82 " --> pdb=" O THR S 69 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 Processing sheet with id= L, first strand: chain 'S' and resid 93 through 99 removed outlier: 3.682A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 140 through 142 removed outlier: 3.580A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.320A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= N 356 hydrogen bonds defined for protein. 1038 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: 2.62 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2899 1.34 - 1.46: 2070 1.46 - 1.58: 4177 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 9248 Sorted by residual: bond pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.26e-02 6.30e+03 7.22e+00 bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.534 1.498 0.036 1.57e-02 4.06e+03 5.25e+00 bond pdb=" CA VAL R 150 " pdb=" CB VAL R 150 " ideal model delta sigma weight residual 1.539 1.528 0.011 5.40e-03 3.43e+04 3.95e+00 bond pdb=" N SER B 331 " pdb=" CA SER B 331 " ideal model delta sigma weight residual 1.455 1.479 -0.023 1.41e-02 5.03e+03 2.74e+00 bond pdb=" CG MET Y 38 " pdb=" SD MET Y 38 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.43e+00 ... (remaining 9243 not shown) Histogram of bond angle deviations from ideal: 99.50 - 106.42: 216 106.42 - 113.33: 4964 113.33 - 120.25: 3329 120.25 - 127.16: 3908 127.16 - 134.08: 103 Bond angle restraints: 12520 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.47 109.24 4.23 1.01e+00 9.80e-01 1.75e+01 angle pdb=" N ILE A 212 " pdb=" CA ILE A 212 " pdb=" C ILE A 212 " ideal model delta sigma weight residual 112.96 109.01 3.95 1.00e+00 1.00e+00 1.56e+01 angle pdb=" CA MET Y 38 " pdb=" CB MET Y 38 " pdb=" CG MET Y 38 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" C LEU Y 37 " pdb=" N MET Y 38 " pdb=" CA MET Y 38 " ideal model delta sigma weight residual 121.14 115.75 5.39 1.75e+00 3.27e-01 9.48e+00 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 112.92 109.20 3.72 1.23e+00 6.61e-01 9.15e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4938 17.91 - 35.82: 440 35.82 - 53.72: 87 53.72 - 71.63: 12 71.63 - 89.54: 6 Dihedral angle restraints: 5483 sinusoidal: 2152 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS S 159 " pdb=" SG CYS S 159 " pdb=" SG CYS S 229 " pdb=" CB CYS S 229 " ideal model delta sinusoidal sigma weight residual -86.00 -113.68 27.68 1 1.00e+01 1.00e-02 1.10e+01 dihedral pdb=" CA ILE R 201 " pdb=" C ILE R 201 " pdb=" N PRO R 202 " pdb=" CA PRO R 202 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG B 150 " pdb=" CD ARG B 150 " pdb=" NE ARG B 150 " pdb=" CZ ARG B 150 " ideal model delta sinusoidal sigma weight residual -180.00 -135.81 -44.19 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 5480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1084 0.047 - 0.094: 250 0.094 - 0.140: 60 0.140 - 0.187: 1 0.187 - 0.234: 2 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CB ILE R 201 " pdb=" CA ILE R 201 " pdb=" CG1 ILE R 201 " pdb=" CG2 ILE R 201 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR A 292 " pdb=" CA THR A 292 " pdb=" OG1 THR A 292 " pdb=" CG2 THR A 292 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA PRO A 299 " pdb=" N PRO A 299 " pdb=" C PRO A 299 " pdb=" CB PRO A 299 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 1394 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 201 " 0.053 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO R 202 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 281 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO R 282 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO R 282 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 282 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO S 151 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " -0.023 5.00e-02 4.00e+02 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1328 2.76 - 3.29: 8777 3.29 - 3.83: 14315 3.83 - 4.36: 16277 4.36 - 4.90: 28874 Nonbonded interactions: 69571 Sorted by model distance: nonbonded pdb=" NE2 GLN A 52 " pdb=" OD1 ASP A 335 " model vdw 2.220 2.520 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.227 2.440 nonbonded pdb=" O ARG A 250 " pdb=" OG1 THR A 251 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR R 56 " pdb=" OD1 ASN R 59 " model vdw 2.271 2.440 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.278 2.440 ... (remaining 69566 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.060 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 27.120 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 0.003 0.050 9248 Z= 0.216 Angle : 0.668 7.608 12520 Z= 0.374 Chirality : 0.042 0.234 1397 Planarity : 0.004 0.079 1584 Dihedral : 13.944 89.539 3326 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.10 % Allowed : 0.41 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.25), residues: 1129 helix: 1.54 (0.27), residues: 393 sheet: -0.72 (0.33), residues: 243 loop : -1.94 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 148 HIS 0.005 0.001 HIS B 266 PHE 0.024 0.001 PHE A 307 TYR 0.009 0.001 TYR S 173 ARG 0.008 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 1.066 Fit side-chains REVERT: A 307 PHE cc_start: 0.8004 (t80) cc_final: 0.7803 (t80) REVERT: B 17 GLN cc_start: 0.9261 (tm-30) cc_final: 0.9056 (tm-30) REVERT: B 295 ASN cc_start: 0.8143 (m-40) cc_final: 0.7904 (m-40) REVERT: B 308 LEU cc_start: 0.8041 (mp) cc_final: 0.7781 (mp) REVERT: R 31 VAL cc_start: 0.8535 (p) cc_final: 0.8286 (p) REVERT: R 222 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6744 (tmm160) REVERT: S 11 LEU cc_start: 0.6560 (pt) cc_final: 0.5728 (tt) REVERT: S 95 TYR cc_start: 0.6714 (m-10) cc_final: 0.6118 (m-10) REVERT: S 227 TYR cc_start: 0.6983 (m-80) cc_final: 0.6499 (m-80) outliers start: 1 outliers final: 0 residues processed: 177 average time/residue: 0.2203 time to fit residues: 54.1762 Evaluate side-chains 147 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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: 0.0980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 293 ASN S 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9248 Z= 0.202 Angle : 0.564 10.398 12520 Z= 0.289 Chirality : 0.042 0.178 1397 Planarity : 0.004 0.055 1584 Dihedral : 4.648 54.503 1252 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.12 % Allowed : 9.13 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1129 helix: 1.72 (0.27), residues: 397 sheet: -0.50 (0.33), residues: 253 loop : -1.93 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.017 0.001 PHE R 165 TYR 0.016 0.001 TYR R 172 ARG 0.007 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 157 time to evaluate : 1.077 Fit side-chains REVERT: B 15 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8682 (pttp) REVERT: B 197 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7497 (mmp80) REVERT: B 295 ASN cc_start: 0.8216 (m-40) cc_final: 0.7807 (m-40) REVERT: S 95 TYR cc_start: 0.6785 (m-10) cc_final: 0.6310 (m-10) REVERT: S 173 TYR cc_start: 0.7720 (m-80) cc_final: 0.7486 (m-80) REVERT: S 174 LEU cc_start: 0.6779 (tp) cc_final: 0.6180 (mp) REVERT: S 227 TYR cc_start: 0.6886 (m-80) cc_final: 0.6421 (m-80) REVERT: Y 44 HIS cc_start: 0.8634 (m90) cc_final: 0.7949 (m-70) outliers start: 11 outliers final: 8 residues processed: 163 average time/residue: 0.2083 time to fit residues: 47.4834 Evaluate side-chains 153 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 144 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR 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: 5.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.0000 chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN S 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9248 Z= 0.190 Angle : 0.564 10.318 12520 Z= 0.283 Chirality : 0.041 0.165 1397 Planarity : 0.004 0.048 1584 Dihedral : 4.570 52.652 1252 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.93 % Allowed : 11.97 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.26), residues: 1129 helix: 1.85 (0.27), residues: 399 sheet: -0.49 (0.32), residues: 265 loop : -1.89 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.001 PHE R 165 TYR 0.019 0.001 TYR R 27 ARG 0.005 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 10 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7575 (pm20) REVERT: B 295 ASN cc_start: 0.8235 (m-40) cc_final: 0.7828 (m-40) REVERT: R 81 MET cc_start: 0.8116 (ttp) cc_final: 0.7834 (ttt) REVERT: R 222 ARG cc_start: 0.7287 (ttp80) cc_final: 0.6771 (tmm160) REVERT: S 95 TYR cc_start: 0.6840 (m-10) cc_final: 0.6432 (m-10) REVERT: S 173 TYR cc_start: 0.7758 (m-80) cc_final: 0.7553 (m-80) REVERT: S 174 LEU cc_start: 0.6785 (tp) cc_final: 0.6196 (mp) REVERT: S 227 TYR cc_start: 0.6827 (m-80) cc_final: 0.6362 (m-80) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.2000 time to fit residues: 48.2804 Evaluate side-chains 160 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 93 GLU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 0.0040 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9248 Z= 0.230 Angle : 0.572 10.640 12520 Z= 0.290 Chirality : 0.042 0.162 1397 Planarity : 0.004 0.049 1584 Dihedral : 4.635 51.058 1252 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.23 % Allowed : 13.08 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1129 helix: 1.86 (0.27), residues: 396 sheet: -0.60 (0.32), residues: 273 loop : -1.91 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.001 PHE R 91 TYR 0.017 0.001 TYR S 103 ARG 0.005 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.033 Fit side-chains REVERT: A 38 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8643 (tt) REVERT: B 10 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: B 295 ASN cc_start: 0.8272 (m-40) cc_final: 0.7858 (m-40) REVERT: S 95 TYR cc_start: 0.6672 (m-10) cc_final: 0.6332 (m-10) REVERT: S 173 TYR cc_start: 0.7774 (m-80) cc_final: 0.7565 (m-80) REVERT: S 174 LEU cc_start: 0.6837 (tp) cc_final: 0.6324 (mp) REVERT: Y 38 MET cc_start: 0.8181 (pmm) cc_final: 0.7966 (pmm) REVERT: Y 44 HIS cc_start: 0.8750 (m90) cc_final: 0.8106 (m170) outliers start: 22 outliers final: 13 residues processed: 172 average time/residue: 0.2037 time to fit residues: 49.5012 Evaluate side-chains 168 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 92 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9248 Z= 0.276 Angle : 0.608 10.774 12520 Z= 0.307 Chirality : 0.043 0.157 1397 Planarity : 0.004 0.051 1584 Dihedral : 4.748 49.911 1252 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.74 % Allowed : 14.81 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1129 helix: 1.67 (0.27), residues: 396 sheet: -0.62 (0.32), residues: 273 loop : -1.93 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.006 0.001 HIS B 91 PHE 0.019 0.002 PHE R 91 TYR 0.021 0.002 TYR R 27 ARG 0.007 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8672 (tt) REVERT: B 10 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: B 17 GLN cc_start: 0.9208 (pp30) cc_final: 0.8898 (pp30) REVERT: B 295 ASN cc_start: 0.8283 (m-40) cc_final: 0.7867 (m-40) REVERT: B 308 LEU cc_start: 0.8080 (mp) cc_final: 0.7878 (mp) REVERT: R 318 MET cc_start: 0.7160 (tpt) cc_final: 0.6704 (ttm) REVERT: S 95 TYR cc_start: 0.6713 (m-10) cc_final: 0.6364 (m-10) REVERT: S 174 LEU cc_start: 0.6873 (tp) cc_final: 0.6410 (mp) REVERT: Y 44 HIS cc_start: 0.8784 (m90) cc_final: 0.8111 (m170) outliers start: 27 outliers final: 16 residues processed: 173 average time/residue: 0.2099 time to fit residues: 50.6579 Evaluate side-chains 169 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain Y residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 50.0000 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.1980 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9248 Z= 0.304 Angle : 0.632 10.701 12520 Z= 0.320 Chirality : 0.043 0.154 1397 Planarity : 0.004 0.053 1584 Dihedral : 4.800 49.109 1252 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.04 % Allowed : 16.23 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1129 helix: 1.58 (0.27), residues: 398 sheet: -0.63 (0.32), residues: 273 loop : -1.95 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.006 0.001 HIS B 91 PHE 0.020 0.002 PHE R 91 TYR 0.021 0.002 TYR R 172 ARG 0.006 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.127 Fit side-chains REVERT: A 38 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8671 (tt) REVERT: B 10 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7438 (pm20) REVERT: B 295 ASN cc_start: 0.8271 (m-40) cc_final: 0.7833 (m-40) REVERT: R 105 MET cc_start: 0.8113 (ttt) cc_final: 0.7774 (ttt) REVERT: R 162 GLU cc_start: 0.8272 (tp30) cc_final: 0.8060 (tp30) REVERT: S 95 TYR cc_start: 0.6737 (m-10) cc_final: 0.6326 (m-10) REVERT: S 174 LEU cc_start: 0.6893 (tp) cc_final: 0.6412 (mp) REVERT: Y 44 HIS cc_start: 0.8800 (m90) cc_final: 0.8096 (m170) outliers start: 30 outliers final: 20 residues processed: 181 average time/residue: 0.2104 time to fit residues: 53.8202 Evaluate side-chains 179 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 VAL Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 67 optimal weight: 0.0970 chunk 65 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9248 Z= 0.148 Angle : 0.598 10.729 12520 Z= 0.293 Chirality : 0.041 0.166 1397 Planarity : 0.004 0.041 1584 Dihedral : 4.524 49.537 1252 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.03 % Allowed : 17.95 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.26), residues: 1129 helix: 2.01 (0.27), residues: 390 sheet: -0.37 (0.32), residues: 271 loop : -1.75 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS A 329 PHE 0.016 0.001 PHE A 307 TYR 0.022 0.001 TYR S 103 ARG 0.007 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8464 (tp) REVERT: B 10 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: B 253 PHE cc_start: 0.8372 (m-10) cc_final: 0.8093 (m-10) REVERT: B 254 ASP cc_start: 0.8400 (t0) cc_final: 0.7540 (p0) REVERT: B 256 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8464 (tpt170) REVERT: B 295 ASN cc_start: 0.8254 (m-40) cc_final: 0.7844 (m-40) REVERT: R 81 MET cc_start: 0.8185 (ttp) cc_final: 0.7823 (ttm) REVERT: R 165 PHE cc_start: 0.5489 (t80) cc_final: 0.5133 (t80) REVERT: R 311 PHE cc_start: 0.7564 (t80) cc_final: 0.7288 (t80) REVERT: S 95 TYR cc_start: 0.6659 (m-10) cc_final: 0.6274 (m-10) REVERT: S 174 LEU cc_start: 0.6930 (tp) cc_final: 0.6489 (mp) REVERT: S 219 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6477 (tt) REVERT: Y 44 HIS cc_start: 0.8717 (m90) cc_final: 0.8076 (m170) outliers start: 20 outliers final: 12 residues processed: 182 average time/residue: 0.1980 time to fit residues: 51.0689 Evaluate side-chains 174 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 159 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Chi-restraints excluded: chain Y residue 51 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9248 Z= 0.217 Angle : 0.630 10.853 12520 Z= 0.311 Chirality : 0.042 0.166 1397 Planarity : 0.004 0.047 1584 Dihedral : 4.609 50.999 1252 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.33 % Allowed : 18.15 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.26), residues: 1129 helix: 1.77 (0.27), residues: 398 sheet: -0.42 (0.32), residues: 273 loop : -1.78 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.020 0.001 PHE A 307 TYR 0.019 0.001 TYR S 103 ARG 0.006 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 163 time to evaluate : 1.194 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8603 (tt) REVERT: B 10 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: B 175 GLN cc_start: 0.7901 (pm20) cc_final: 0.7594 (pm20) REVERT: B 295 ASN cc_start: 0.8298 (m-40) cc_final: 0.7891 (m-40) REVERT: R 81 MET cc_start: 0.8222 (ttp) cc_final: 0.7889 (ttm) REVERT: S 29 PHE cc_start: 0.7470 (t80) cc_final: 0.6876 (t80) REVERT: S 95 TYR cc_start: 0.6666 (m-10) cc_final: 0.6346 (m-10) REVERT: S 174 LEU cc_start: 0.6885 (tp) cc_final: 0.6434 (mp) REVERT: S 219 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6462 (tt) REVERT: Y 44 HIS cc_start: 0.8780 (m90) cc_final: 0.8102 (m170) outliers start: 23 outliers final: 19 residues processed: 177 average time/residue: 0.2064 time to fit residues: 51.2473 Evaluate side-chains 182 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 0.0370 chunk 103 optimal weight: 0.2980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9248 Z= 0.177 Angle : 0.624 10.921 12520 Z= 0.307 Chirality : 0.042 0.177 1397 Planarity : 0.004 0.044 1584 Dihedral : 4.544 50.511 1252 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.43 % Allowed : 18.26 % Favored : 79.31 % 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: -0.15 (0.26), residues: 1129 helix: 1.82 (0.27), residues: 397 sheet: -0.29 (0.33), residues: 271 loop : -1.74 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.016 0.001 PHE R 91 TYR 0.024 0.001 TYR S 103 ARG 0.006 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8472 (tp) REVERT: B 10 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7485 (pm20) REVERT: B 17 GLN cc_start: 0.9008 (pp30) cc_final: 0.8549 (pp30) REVERT: B 175 GLN cc_start: 0.7882 (pm20) cc_final: 0.7554 (pm20) REVERT: B 253 PHE cc_start: 0.8393 (m-10) cc_final: 0.8109 (m-10) REVERT: B 254 ASP cc_start: 0.8467 (t0) cc_final: 0.7600 (p0) REVERT: B 256 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7450 (tpt90) REVERT: B 295 ASN cc_start: 0.8273 (m-40) cc_final: 0.7886 (m-40) REVERT: R 81 MET cc_start: 0.8184 (ttp) cc_final: 0.7867 (ttm) REVERT: R 311 PHE cc_start: 0.7477 (t80) cc_final: 0.7262 (t80) REVERT: R 317 MET cc_start: 0.7536 (tmm) cc_final: 0.7256 (tmm) REVERT: S 29 PHE cc_start: 0.7447 (t80) cc_final: 0.6862 (t80) REVERT: S 95 TYR cc_start: 0.6656 (m-10) cc_final: 0.6372 (m-10) REVERT: S 174 LEU cc_start: 0.6913 (tp) cc_final: 0.6447 (mp) REVERT: S 219 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6439 (tt) REVERT: Y 44 HIS cc_start: 0.8692 (m90) cc_final: 0.8042 (m170) outliers start: 24 outliers final: 18 residues processed: 179 average time/residue: 0.2081 time to fit residues: 52.2385 Evaluate side-chains 181 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 94 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9248 Z= 0.222 Angle : 0.642 10.856 12520 Z= 0.318 Chirality : 0.043 0.181 1397 Planarity : 0.004 0.044 1584 Dihedral : 4.629 51.206 1252 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.33 % Allowed : 19.07 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.26), residues: 1129 helix: 1.74 (0.27), residues: 397 sheet: -0.40 (0.33), residues: 275 loop : -1.73 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.001 PHE R 91 TYR 0.024 0.001 TYR S 103 ARG 0.006 0.000 ARG R 222 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8610 (tt) REVERT: B 10 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7474 (pm20) REVERT: B 295 ASN cc_start: 0.8306 (m-40) cc_final: 0.7926 (m-40) REVERT: R 81 MET cc_start: 0.8212 (ttp) cc_final: 0.7885 (ttm) REVERT: R 105 MET cc_start: 0.8034 (ttt) cc_final: 0.7635 (ttt) REVERT: R 317 MET cc_start: 0.7495 (tmm) cc_final: 0.7221 (tmm) REVERT: S 29 PHE cc_start: 0.7447 (t80) cc_final: 0.6880 (t80) REVERT: S 95 TYR cc_start: 0.6673 (m-10) cc_final: 0.6403 (m-10) REVERT: S 174 LEU cc_start: 0.6866 (tp) cc_final: 0.6458 (mt) REVERT: S 219 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6374 (tt) REVERT: Y 44 HIS cc_start: 0.8700 (m90) cc_final: 0.8057 (m170) outliers start: 23 outliers final: 19 residues processed: 178 average time/residue: 0.2051 time to fit residues: 51.2484 Evaluate side-chains 184 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ARG Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 209 VAL Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 302 MET Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 219 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.205021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.134359 restraints weight = 11653.727| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 3.01 r_work: 0.3483 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9248 Z= 0.170 Angle : 0.623 10.971 12520 Z= 0.307 Chirality : 0.042 0.179 1397 Planarity : 0.004 0.043 1584 Dihedral : 4.524 50.961 1252 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.43 % Allowed : 18.46 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1129 helix: 1.81 (0.27), residues: 397 sheet: -0.22 (0.33), residues: 270 loop : -1.69 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS S 35 PHE 0.016 0.001 PHE R 91 TYR 0.024 0.001 TYR S 103 ARG 0.006 0.000 ARG R 222 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2352.67 seconds wall clock time: 43 minutes 34.53 seconds (2614.53 seconds total)