Starting phenix.real_space_refine on Fri Nov 15 12:10:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j20_35940/11_2024/8j20_35940.cif" } resolution = 3.2 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= 0.020 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: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 2 4.86 5 C 5634 2.51 5 N 1497 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2610 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "B" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1775 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Chain: "D" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2188 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 13, 'TRANS': 260} Chain breaks: 1 Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'9T4': 1, 'LEA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.35, per 1000 atoms: 0.61 Number of scatterers: 8832 At special positions: 0 Unit cell: (111.28, 110.24, 122.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 58 16.00 O 1641 8.00 N 1497 7.00 C 5634 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 267 " distance=2.04 Simple disulfide: pdb=" SG CYS D 88 " - pdb=" SG CYS D 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2092 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 37.6% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 15 through 36 removed outlier: 3.595A pdb=" N CYS A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.504A pdb=" N ILE A 44 " --> pdb=" O THR A 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 94 removed outlier: 3.936A pdb=" N GLY B 94 " --> pdb=" O SER B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.551A pdb=" N LYS B 103 " --> pdb=" O ASP B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.015A pdb=" N THR B 129 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 6 removed outlier: 3.766A pdb=" N SER C 6 " --> pdb=" O CYS C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 7 through 32 removed outlier: 3.661A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.372A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 255 removed outlier: 3.728A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.596A pdb=" N GLU C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 310 removed outlier: 4.029A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 351 Processing helix chain 'D' and resid 14 through 46 removed outlier: 3.707A pdb=" N VAL D 20 " --> pdb=" O LEU D 16 " (cutoff:3.500A) Proline residue: D 30 - end of helix removed outlier: 3.958A pdb=" N VAL D 37 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 73 removed outlier: 3.623A pdb=" N ASP D 61 " --> pdb=" O LEU D 57 " (cutoff:3.500A) Proline residue: D 69 - end of helix Processing helix chain 'D' and resid 87 through 119 removed outlier: 3.522A pdb=" N TYR D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU D 104 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 117 " --> pdb=" O ARG D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 126 Processing helix chain 'D' and resid 128 through 155 removed outlier: 3.736A pdb=" N VAL D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE D 155 " --> pdb=" O TYR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 211 Proline residue: D 183 - end of helix removed outlier: 3.880A pdb=" N VAL D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Proline residue: D 196 - end of helix Processing helix chain 'D' and resid 216 through 252 removed outlier: 4.438A pdb=" N ARG D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.766A pdb=" N TYR D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 280 removed outlier: 4.044A pdb=" N VAL D 261 " --> pdb=" O TRP D 257 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Proline residue: D 273 - end of helix removed outlier: 3.584A pdb=" N PHE D 278 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER D 280 " --> pdb=" O TYR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 291 removed outlier: 3.826A pdb=" N GLU D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 24 removed outlier: 3.654A pdb=" N GLN E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.064A pdb=" N LEU A 90 " --> pdb=" O ALA A 103 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A 103 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE A 92 " --> pdb=" O VAL A 101 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 126 removed outlier: 6.407A pdb=" N CYS A 132 " --> pdb=" O GLU A 149 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 149 " --> pdb=" O CYS A 132 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 134 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 145 " --> pdb=" O ASN A 136 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.524A pdb=" N THR A 189 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASP A 181 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLN A 187 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.651A pdb=" N PHE A 210 " --> pdb=" O TRP A 222 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 231 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A 223 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS A 229 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 243 removed outlier: 3.739A pdb=" N SER A 256 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS A 261 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR A 274 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A 263 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN A 270 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 284 through 289 removed outlier: 4.665A pdb=" N VAL A 287 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 297 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE A 289 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU A 295 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N CYS A 305 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL A 318 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 307 " --> pdb=" O ALA A 316 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 3.587A pdb=" N THR B 116 " --> pdb=" O ASP B 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.151A pdb=" N GLY B 48 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET B 72 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR B 88 " --> pdb=" O MET B 72 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP B 74 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.151A pdb=" N GLY B 48 " --> pdb=" O THR B 156 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE B 148 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AB3, first strand: chain 'B' and resid 184 through 185 removed outlier: 3.541A pdb=" N GLY B 263 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 212 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR B 228 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP B 214 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 196 through 200 removed outlier: 6.490A pdb=" N LYS C 35 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE C 222 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LEU C 37 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N CYS C 224 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 39 " --> pdb=" O CYS C 224 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ALA C 226 " --> pdb=" O LEU C 39 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1143 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: 2.48 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1425 1.31 - 1.44: 2509 1.44 - 1.56: 5002 1.56 - 1.69: 2 1.69 - 1.82: 84 Bond restraints: 9022 Sorted by residual: bond pdb=" C13 9T4 D 401 " pdb=" C16 9T4 D 401 " ideal model delta sigma weight residual 1.342 1.523 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C09 9T4 D 401 " pdb=" C10 9T4 D 401 " ideal model delta sigma weight residual 1.359 1.523 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" C27 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.384 1.529 -0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" C26 9T4 D 401 " pdb=" C28 9T4 D 401 " ideal model delta sigma weight residual 1.386 1.529 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C24 9T4 D 401 " pdb=" C27 9T4 D 401 " ideal model delta sigma weight residual 1.385 1.528 -0.143 2.00e-02 2.50e+03 5.08e+01 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.99: 12180 3.99 - 7.99: 37 7.99 - 11.98: 3 11.98 - 15.98: 3 15.98 - 19.97: 3 Bond angle restraints: 12226 Sorted by residual: angle pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta sigma weight residual 119.84 132.52 -12.68 1.25e+00 6.40e-01 1.03e+02 angle pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" C TYR B 273 " ideal model delta sigma weight residual 109.81 129.78 -19.97 2.21e+00 2.05e-01 8.17e+01 angle pdb=" C PRO B 274 " pdb=" CA PRO B 274 " pdb=" CB PRO B 274 " ideal model delta sigma weight residual 111.56 124.57 -13.01 1.65e+00 3.67e-01 6.22e+01 angle pdb=" C GLU B 272 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " ideal model delta sigma weight residual 121.80 135.07 -13.27 2.44e+00 1.68e-01 2.96e+01 angle pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" CD PRO B 274 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 ... (remaining 12221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.59: 4776 23.59 - 47.18: 502 47.18 - 70.77: 65 70.77 - 94.37: 9 94.37 - 117.96: 1 Dihedral angle restraints: 5353 sinusoidal: 2103 harmonic: 3250 Sorted by residual: dihedral pdb=" CA TYR B 273 " pdb=" C TYR B 273 " pdb=" N PRO B 274 " pdb=" CA PRO B 274 " ideal model delta harmonic sigma weight residual 180.00 62.04 117.96 0 5.00e+00 4.00e-02 5.57e+02 dihedral pdb=" C TYR B 273 " pdb=" N TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual -122.60 -150.58 27.98 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CA TYR B 273 " pdb=" CB TYR B 273 " ideal model delta harmonic sigma weight residual 122.80 150.30 -27.50 0 2.50e+00 1.60e-01 1.21e+02 ... (remaining 5350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.257: 1380 0.257 - 0.514: 0 0.514 - 0.771: 1 0.771 - 1.028: 0 1.028 - 1.286: 1 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA TYR B 273 " pdb=" N TYR B 273 " pdb=" C TYR B 273 " pdb=" CB TYR B 273 " both_signs ideal model delta sigma weight residual False 2.51 1.22 1.29 2.00e-01 2.50e+01 4.13e+01 chirality pdb=" CA PRO B 274 " pdb=" N PRO B 274 " pdb=" C PRO B 274 " pdb=" CB PRO B 274 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C08 9T4 D 401 " pdb=" C09 9T4 D 401 " pdb=" C13 9T4 D 401 " pdb=" C17 9T4 D 401 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1379 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 273 " -0.066 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO B 274 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 272 " 0.058 5.00e-02 4.00e+02 8.75e-02 1.23e+01 pdb=" N PRO D 273 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO D 273 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 273 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 239 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 240 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 240 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 240 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 675 2.74 - 3.28: 8615 3.28 - 3.82: 14912 3.82 - 4.36: 17012 4.36 - 4.90: 29893 Nonbonded interactions: 71107 Sorted by model distance: nonbonded pdb=" OH TYR B 211 " pdb=" OG SER C 6 " model vdw 2.197 3.040 nonbonded pdb=" OG SER A 342 " pdb=" OD1 ASP A 344 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 172 " pdb=" OD1 ASP A 174 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.265 3.040 nonbonded pdb=" O LEU D 197 " pdb=" OG SER D 201 " model vdw 2.269 3.040 ... (remaining 71102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.99 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.760 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 : 0.006 0.181 9022 Z= 0.403 Angle : 0.709 19.972 12226 Z= 0.355 Chirality : 0.057 1.286 1382 Planarity : 0.005 0.097 1544 Dihedral : 17.895 117.958 3252 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.54 % Allowed : 4.43 % Favored : 95.03 % Rotamer: Outliers : 0.62 % Allowed : 35.69 % Favored : 63.68 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.09 % 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: 0.12 (0.26), residues: 1107 helix: 1.66 (0.28), residues: 355 sheet: 0.71 (0.33), residues: 243 loop : -1.45 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 15 HIS 0.006 0.001 HIS B 205 PHE 0.017 0.001 PHE A 210 TYR 0.011 0.001 TYR D 202 ARG 0.007 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7726 (mm110) REVERT: A 163 LEU cc_start: 0.7931 (mm) cc_final: 0.7715 (mt) outliers start: 6 outliers final: 3 residues processed: 199 average time/residue: 0.2645 time to fit residues: 68.8090 Evaluate side-chains 195 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 220 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN B 180 GLN B 217 GLN C 195 HIS C 241 ASN D 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9022 Z= 0.260 Angle : 0.674 13.397 12226 Z= 0.341 Chirality : 0.046 0.359 1382 Planarity : 0.005 0.062 1544 Dihedral : 6.074 58.363 1268 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Rotamer: Outliers : 5.20 % Allowed : 29.76 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.00 (0.26), residues: 1107 helix: 1.37 (0.27), residues: 381 sheet: 0.65 (0.34), residues: 243 loop : -1.52 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 85 HIS 0.006 0.001 HIS A 102 PHE 0.023 0.002 PHE D 95 TYR 0.015 0.002 TYR B 88 ARG 0.006 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 61 THR cc_start: 0.5128 (OUTLIER) cc_final: 0.4343 (m) REVERT: A 72 MET cc_start: 0.7045 (mmt) cc_final: 0.6799 (mmt) REVERT: A 140 ARG cc_start: 0.7189 (mtp85) cc_final: 0.6912 (mmp80) REVERT: A 269 ASP cc_start: 0.7800 (t0) cc_final: 0.7519 (t0) REVERT: A 297 LEU cc_start: 0.8241 (mp) cc_final: 0.8023 (mp) REVERT: A 326 VAL cc_start: 0.8041 (t) cc_final: 0.7785 (p) REVERT: B 268 MET cc_start: 0.8251 (ttm) cc_final: 0.7957 (ttm) REVERT: C 200 ASP cc_start: 0.7902 (t0) cc_final: 0.7646 (t0) REVERT: C 283 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7966 (mp) REVERT: C 306 GLN cc_start: 0.6432 (mm110) cc_final: 0.6157 (mm110) REVERT: C 316 THR cc_start: 0.7671 (p) cc_final: 0.7378 (t) REVERT: D 29 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7337 (mt) REVERT: D 56 ASN cc_start: 0.7289 (m-40) cc_final: 0.7027 (m-40) outliers start: 50 outliers final: 25 residues processed: 255 average time/residue: 0.2287 time to fit residues: 78.0267 Evaluate side-chains 238 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7277 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9022 Z= 0.223 Angle : 0.628 14.056 12226 Z= 0.316 Chirality : 0.045 0.278 1382 Planarity : 0.004 0.053 1544 Dihedral : 5.839 54.941 1264 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.79 % Favored : 94.76 % Rotamer: Outliers : 5.52 % Allowed : 30.28 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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 (0.25), residues: 1107 helix: 1.20 (0.27), residues: 391 sheet: 0.27 (0.33), residues: 262 loop : -1.49 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.003 0.001 HIS B 73 PHE 0.017 0.001 PHE A 210 TYR 0.015 0.001 TYR B 141 ARG 0.004 0.000 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 215 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 112 MET cc_start: 0.7424 (ptp) cc_final: 0.7127 (ptp) REVERT: A 135 TYR cc_start: 0.8878 (m-80) cc_final: 0.8422 (m-80) REVERT: A 269 ASP cc_start: 0.7757 (t0) cc_final: 0.7412 (t0) REVERT: A 326 VAL cc_start: 0.8170 (t) cc_final: 0.7904 (p) REVERT: B 268 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: C 17 LYS cc_start: 0.8344 (mttm) cc_final: 0.8104 (mmtm) REVERT: C 33 GLU cc_start: 0.6919 (tt0) cc_final: 0.6563 (tt0) REVERT: C 197 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7108 (mttm) REVERT: C 200 ASP cc_start: 0.8008 (t0) cc_final: 0.7650 (t0) REVERT: C 245 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6747 (tm-30) REVERT: C 306 GLN cc_start: 0.6517 (mm110) cc_final: 0.6151 (mm110) REVERT: C 316 THR cc_start: 0.7673 (p) cc_final: 0.7382 (t) REVERT: D 29 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7099 (mt) REVERT: D 56 ASN cc_start: 0.7301 (m-40) cc_final: 0.6994 (m-40) REVERT: D 66 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6602 (pp) outliers start: 53 outliers final: 30 residues processed: 250 average time/residue: 0.2412 time to fit residues: 79.9425 Evaluate side-chains 242 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 337 ASP Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 247 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 60 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9022 Z= 0.256 Angle : 0.657 13.819 12226 Z= 0.327 Chirality : 0.045 0.283 1382 Planarity : 0.005 0.089 1544 Dihedral : 5.775 51.976 1264 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 5.93 % Allowed : 30.18 % Favored : 63.89 % 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: -0.26 (0.25), residues: 1107 helix: 1.17 (0.27), residues: 391 sheet: 0.05 (0.32), residues: 257 loop : -1.49 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 180 HIS 0.004 0.001 HIS A 102 PHE 0.015 0.002 PHE A 210 TYR 0.014 0.002 TYR B 141 ARG 0.008 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 86 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7927 (mm-40) REVERT: A 112 MET cc_start: 0.7397 (ptp) cc_final: 0.7099 (ptp) REVERT: A 135 TYR cc_start: 0.8879 (m-80) cc_final: 0.8466 (m-80) REVERT: A 192 THR cc_start: 0.8075 (p) cc_final: 0.7812 (p) REVERT: A 269 ASP cc_start: 0.7776 (t0) cc_final: 0.7384 (t0) REVERT: B 268 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: C 17 LYS cc_start: 0.8338 (mttm) cc_final: 0.8091 (mmtm) REVERT: C 197 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (mttm) REVERT: C 200 ASP cc_start: 0.8021 (t0) cc_final: 0.7679 (t0) REVERT: C 245 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6664 (tm-30) REVERT: C 283 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8140 (mp) REVERT: C 306 GLN cc_start: 0.6523 (mm110) cc_final: 0.6183 (mm110) REVERT: C 316 THR cc_start: 0.7739 (p) cc_final: 0.7433 (t) REVERT: D 18 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6582 (p90) REVERT: D 29 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7303 (mt) REVERT: D 52 VAL cc_start: 0.7646 (OUTLIER) cc_final: 0.7271 (m) REVERT: D 56 ASN cc_start: 0.7352 (m-40) cc_final: 0.7091 (m-40) REVERT: D 66 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6685 (pp) REVERT: D 71 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6486 (ttp-110) outliers start: 57 outliers final: 36 residues processed: 242 average time/residue: 0.2459 time to fit residues: 79.3169 Evaluate side-chains 247 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 MET Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 197 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 44 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9022 Z= 0.217 Angle : 0.627 14.151 12226 Z= 0.315 Chirality : 0.044 0.250 1382 Planarity : 0.005 0.083 1544 Dihedral : 5.777 53.526 1264 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.88 % Favored : 94.67 % Rotamer: Outliers : 5.93 % Allowed : 29.34 % Favored : 64.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1107 helix: 1.20 (0.27), residues: 391 sheet: -0.05 (0.31), residues: 264 loop : -1.49 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 140 HIS 0.003 0.001 HIS B 73 PHE 0.017 0.001 PHE A 210 TYR 0.015 0.001 TYR B 228 ARG 0.010 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 0.948 Fit side-chains REVERT: A 135 TYR cc_start: 0.8855 (m-80) cc_final: 0.8476 (m-80) REVERT: A 192 THR cc_start: 0.8085 (p) cc_final: 0.7819 (p) REVERT: A 230 ARG cc_start: 0.7562 (mtm180) cc_final: 0.7249 (mtm180) REVERT: A 269 ASP cc_start: 0.7766 (t0) cc_final: 0.7407 (t0) REVERT: C 17 LYS cc_start: 0.8302 (mttm) cc_final: 0.8085 (mmtm) REVERT: C 200 ASP cc_start: 0.8011 (t0) cc_final: 0.7718 (t0) REVERT: C 245 GLU cc_start: 0.6971 (tm-30) cc_final: 0.6630 (tm-30) REVERT: C 306 GLN cc_start: 0.6523 (mm110) cc_final: 0.6158 (mm110) REVERT: D 18 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6576 (p90) REVERT: D 29 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7268 (mt) REVERT: D 52 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7294 (m) REVERT: D 66 LEU cc_start: 0.6864 (OUTLIER) cc_final: 0.6629 (pp) REVERT: D 71 ARG cc_start: 0.6829 (ttp80) cc_final: 0.6444 (ttp-110) REVERT: D 278 PHE cc_start: 0.6480 (p90) cc_final: 0.6184 (p90) outliers start: 57 outliers final: 40 residues processed: 245 average time/residue: 0.2471 time to fit residues: 79.9259 Evaluate side-chains 259 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 215 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 166 ASN C 331 ASN E 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9022 Z= 0.301 Angle : 0.668 13.745 12226 Z= 0.336 Chirality : 0.045 0.267 1382 Planarity : 0.005 0.080 1544 Dihedral : 5.928 51.955 1264 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 7.08 % Allowed : 28.72 % Favored : 64.20 % 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: -0.46 (0.25), residues: 1107 helix: 1.01 (0.27), residues: 396 sheet: -0.14 (0.31), residues: 258 loop : -1.58 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 180 HIS 0.005 0.001 HIS C 195 PHE 0.018 0.002 PHE A 210 TYR 0.016 0.002 TYR A 96 ARG 0.011 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 222 time to evaluate : 0.945 Fit side-chains REVERT: A 135 TYR cc_start: 0.8874 (m-80) cc_final: 0.8514 (m-80) REVERT: A 158 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7506 (p) REVERT: A 192 THR cc_start: 0.8256 (p) cc_final: 0.7995 (p) REVERT: A 230 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7190 (mtm180) REVERT: A 265 ASP cc_start: 0.6984 (t70) cc_final: 0.6767 (t70) REVERT: A 269 ASP cc_start: 0.7803 (t0) cc_final: 0.7394 (t0) REVERT: B 155 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6838 (tt) REVERT: C 17 LYS cc_start: 0.8317 (mttm) cc_final: 0.8104 (mmtm) REVERT: C 33 GLU cc_start: 0.7126 (tt0) cc_final: 0.6840 (tt0) REVERT: C 189 PHE cc_start: 0.7734 (p90) cc_final: 0.7228 (p90) REVERT: C 197 LYS cc_start: 0.7867 (mttm) cc_final: 0.7291 (mttm) REVERT: C 200 ASP cc_start: 0.8088 (t0) cc_final: 0.7821 (t0) REVERT: C 245 GLU cc_start: 0.6986 (tm-30) cc_final: 0.6635 (tm-30) REVERT: C 277 LYS cc_start: 0.7343 (tttm) cc_final: 0.7113 (tttm) REVERT: D 18 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6759 (p90) REVERT: D 29 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7316 (mt) REVERT: D 52 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7312 (m) REVERT: D 66 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6720 (pp) REVERT: D 83 LEU cc_start: 0.5726 (mm) cc_final: 0.5524 (pt) outliers start: 68 outliers final: 49 residues processed: 255 average time/residue: 0.2664 time to fit residues: 90.1699 Evaluate side-chains 271 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 66 optimal weight: 0.0060 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 231 GLN C 322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.209 Angle : 0.635 14.723 12226 Z= 0.318 Chirality : 0.044 0.243 1382 Planarity : 0.005 0.077 1544 Dihedral : 5.903 55.079 1264 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.33 % Favored : 94.22 % Rotamer: Outliers : 7.08 % Allowed : 29.03 % Favored : 63.89 % 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: -0.42 (0.25), residues: 1107 helix: 1.06 (0.27), residues: 396 sheet: -0.13 (0.32), residues: 252 loop : -1.55 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 180 HIS 0.004 0.001 HIS A 73 PHE 0.036 0.002 PHE D 278 TYR 0.015 0.001 TYR B 141 ARG 0.014 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 220 time to evaluate : 0.962 Fit side-chains REVERT: A 135 TYR cc_start: 0.8837 (m-80) cc_final: 0.8560 (m-80) REVERT: A 158 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7399 (p) REVERT: A 192 THR cc_start: 0.8131 (p) cc_final: 0.7850 (p) REVERT: A 230 ARG cc_start: 0.7435 (mtm180) cc_final: 0.7207 (mtm180) REVERT: A 269 ASP cc_start: 0.7797 (t0) cc_final: 0.7426 (t0) REVERT: B 155 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6709 (tt) REVERT: C 17 LYS cc_start: 0.8292 (mttm) cc_final: 0.8076 (mmtm) REVERT: C 200 ASP cc_start: 0.8054 (t0) cc_final: 0.7753 (t0) REVERT: C 245 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6619 (tm-30) REVERT: C 317 LYS cc_start: 0.7365 (mtmm) cc_final: 0.7148 (ttmm) REVERT: D 18 PHE cc_start: 0.7011 (OUTLIER) cc_final: 0.6764 (p90) REVERT: D 29 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7268 (mt) REVERT: D 52 VAL cc_start: 0.7727 (p) cc_final: 0.7334 (m) REVERT: D 59 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7721 (pt) REVERT: D 66 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6661 (pp) outliers start: 68 outliers final: 44 residues processed: 254 average time/residue: 0.2592 time to fit residues: 87.4614 Evaluate side-chains 261 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 121 MET Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 290 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.0060 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9022 Z= 0.203 Angle : 0.630 14.584 12226 Z= 0.316 Chirality : 0.044 0.286 1382 Planarity : 0.005 0.066 1544 Dihedral : 5.806 56.195 1262 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.24 % Favored : 94.40 % Rotamer: Outliers : 6.56 % Allowed : 29.14 % Favored : 64.31 % 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: -0.32 (0.25), residues: 1107 helix: 1.21 (0.27), residues: 389 sheet: -0.09 (0.31), residues: 256 loop : -1.54 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 180 HIS 0.003 0.001 HIS C 195 PHE 0.034 0.002 PHE C 189 TYR 0.019 0.001 TYR B 273 ARG 0.012 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 213 time to evaluate : 1.001 Fit side-chains REVERT: A 135 TYR cc_start: 0.8818 (m-80) cc_final: 0.8491 (m-80) REVERT: A 192 THR cc_start: 0.8101 (p) cc_final: 0.7817 (p) REVERT: A 209 LEU cc_start: 0.8228 (mt) cc_final: 0.8005 (mp) REVERT: A 269 ASP cc_start: 0.7818 (t0) cc_final: 0.7361 (t0) REVERT: B 155 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6667 (tt) REVERT: C 17 LYS cc_start: 0.8290 (mttm) cc_final: 0.8064 (mmtm) REVERT: C 189 PHE cc_start: 0.7544 (p90) cc_final: 0.6952 (p90) REVERT: C 200 ASP cc_start: 0.8054 (t0) cc_final: 0.7752 (t0) REVERT: C 245 GLU cc_start: 0.6990 (tm-30) cc_final: 0.6660 (tm-30) REVERT: C 317 LYS cc_start: 0.7280 (mtmm) cc_final: 0.6975 (ttpt) REVERT: D 18 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6749 (p90) REVERT: D 29 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7254 (mt) REVERT: D 52 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7368 (m) REVERT: D 59 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7730 (pt) outliers start: 63 outliers final: 46 residues processed: 246 average time/residue: 0.2476 time to fit residues: 80.6152 Evaluate side-chains 256 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.0670 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN D 146 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9022 Z= 0.215 Angle : 0.643 14.925 12226 Z= 0.320 Chirality : 0.045 0.277 1382 Planarity : 0.005 0.072 1544 Dihedral : 5.875 56.166 1262 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.42 % Favored : 94.22 % Rotamer: Outliers : 6.14 % Allowed : 29.97 % Favored : 63.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1107 helix: 1.29 (0.27), residues: 383 sheet: -0.09 (0.31), residues: 257 loop : -1.53 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 180 HIS 0.003 0.001 HIS B 73 PHE 0.029 0.002 PHE D 278 TYR 0.014 0.001 TYR B 141 ARG 0.010 0.001 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 210 time to evaluate : 0.997 Fit side-chains REVERT: A 135 TYR cc_start: 0.8808 (m-80) cc_final: 0.8425 (m-80) REVERT: A 192 THR cc_start: 0.8085 (p) cc_final: 0.7803 (p) REVERT: A 269 ASP cc_start: 0.7810 (t0) cc_final: 0.7359 (t0) REVERT: B 155 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6676 (tt) REVERT: C 189 PHE cc_start: 0.7544 (p90) cc_final: 0.6985 (p90) REVERT: C 200 ASP cc_start: 0.8052 (t0) cc_final: 0.7753 (t0) REVERT: C 245 GLU cc_start: 0.6987 (tm-30) cc_final: 0.6602 (tm-30) REVERT: C 317 LYS cc_start: 0.7321 (mtmm) cc_final: 0.7013 (ttpt) REVERT: D 18 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6752 (p90) REVERT: D 29 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7252 (mt) REVERT: D 52 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7285 (m) REVERT: D 59 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7720 (pt) REVERT: D 220 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6107 (mpp-170) outliers start: 59 outliers final: 46 residues processed: 244 average time/residue: 0.2339 time to fit residues: 75.2504 Evaluate side-chains 258 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 220 ARG Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9022 Z= 0.267 Angle : 0.684 14.538 12226 Z= 0.341 Chirality : 0.046 0.273 1382 Planarity : 0.005 0.074 1544 Dihedral : 6.051 55.272 1262 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.51 % Favored : 94.13 % Rotamer: Outliers : 5.52 % Allowed : 31.11 % Favored : 63.37 % 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 (0.25), residues: 1107 helix: 1.07 (0.27), residues: 392 sheet: -0.26 (0.32), residues: 244 loop : -1.64 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.005 0.001 HIS D 245 PHE 0.030 0.002 PHE D 278 TYR 0.017 0.002 TYR B 141 ARG 0.010 0.001 ARG D 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 214 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 135 TYR cc_start: 0.8822 (m-80) cc_final: 0.8472 (m-80) REVERT: A 192 THR cc_start: 0.8109 (p) cc_final: 0.7831 (p) REVERT: A 269 ASP cc_start: 0.7793 (t0) cc_final: 0.7354 (t0) REVERT: B 155 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6706 (tt) REVERT: C 17 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8140 (mmtm) REVERT: C 189 PHE cc_start: 0.7595 (p90) cc_final: 0.7025 (p90) REVERT: C 200 ASP cc_start: 0.8075 (t0) cc_final: 0.7763 (t0) REVERT: C 245 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6652 (tm-30) REVERT: C 317 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7292 (ttmt) REVERT: D 18 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6717 (p90) REVERT: D 29 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7087 (mt) REVERT: D 52 VAL cc_start: 0.7681 (OUTLIER) cc_final: 0.7299 (m) REVERT: D 59 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7736 (pt) outliers start: 53 outliers final: 44 residues processed: 245 average time/residue: 0.2500 time to fit residues: 81.3939 Evaluate side-chains 256 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 341 ASP Chi-restraints excluded: chain D residue 18 PHE Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 151 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 188 MET Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain E residue 9 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 231 GLN C 188 HIS C 294 ASN C 322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131499 restraints weight = 13018.860| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.11 r_work: 0.3491 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9022 Z= 0.249 Angle : 0.676 14.722 12226 Z= 0.334 Chirality : 0.046 0.272 1382 Planarity : 0.005 0.075 1544 Dihedral : 6.121 57.750 1262 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.51 % Favored : 94.13 % Rotamer: Outliers : 6.35 % Allowed : 30.39 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.25), residues: 1107 helix: 1.04 (0.27), residues: 392 sheet: -0.24 (0.32), residues: 250 loop : -1.62 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 180 HIS 0.004 0.001 HIS D 245 PHE 0.028 0.002 PHE D 278 TYR 0.019 0.002 TYR B 141 ARG 0.008 0.001 ARG D 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2618.07 seconds wall clock time: 48 minutes 18.03 seconds (2898.03 seconds total)