Starting phenix.real_space_refine on Mon Mar 11 11:43:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6s8h_10122/03_2024/6s8h_10122_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 43 5.16 5 C 5068 2.51 5 N 1285 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 86": "OE1" <-> "OE2" Residue "A GLU 112": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 194": "OD1" <-> "OD2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B GLU 86": "OE1" <-> "OE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "B ASP 227": "OD1" <-> "OD2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F ASP 40": "OD1" <-> "OD2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ARG 295": "NH1" <-> "NH2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 8": "OD1" <-> "OD2" Residue "G ASP 37": "OD1" <-> "OD2" Residue "G PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7818 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1868 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 8, 'TRANS': 230} Chain: "B" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1857 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "F" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1864 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 9, 'TRANS': 229} Chain breaks: 1 Chain: "G" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1876 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 11, 'TRANS': 231} Chain breaks: 2 Chain: "F" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 281 Unusual residues: {'DCQ': 1, 'JSG': 1, 'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 21 Chain: "G" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {'DCQ': 1, 'LMN': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 25 Time building chain proxies: 6.93, per 1000 atoms: 0.89 Number of scatterers: 7818 At special positions: 0 Unit cell: (114.582, 77.064, 95.316, 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) S 43 16.00 P 4 15.00 O 1418 8.00 N 1285 7.00 C 5068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 6 sheets defined 40.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 removed outlier: 3.723A pdb=" N VAL A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 No H-bonds generated for 'chain 'A' and resid 72 through 75' Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.963A pdb=" N LEU A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 151 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.865A pdb=" N THR B 44 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR B 45 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 49 " --> pdb=" O PHE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 95 through 103 removed outlier: 4.067A pdb=" N VAL B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.649A pdb=" N ALA B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.710A pdb=" N ASP B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 removed outlier: 3.958A pdb=" N LEU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.821A pdb=" N LYS F 13 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 36 removed outlier: 3.521A pdb=" N ARG F 33 " --> pdb=" O GLN F 29 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY F 36 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.843A pdb=" N LEU F 52 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.392A pdb=" N GLN F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix removed outlier: 3.887A pdb=" N LEU F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 99 No H-bonds generated for 'chain 'F' and resid 96 through 99' Processing helix chain 'F' and resid 104 through 117 removed outlier: 3.991A pdb=" N PHE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL F 112 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 115 " --> pdb=" O ILE F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 271 through 279 removed outlier: 4.312A pdb=" N VAL F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE F 277 " --> pdb=" O VAL F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 315 removed outlier: 3.524A pdb=" N LEU F 300 " --> pdb=" O LEU F 297 " (cutoff:3.500A) Proline residue: F 301 - end of helix removed outlier: 4.232A pdb=" N LEU F 304 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU F 308 " --> pdb=" O LEU F 305 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE F 310 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 311 " --> pdb=" O LEU F 308 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLN F 313 " --> pdb=" O PHE F 310 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR F 314 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 344 removed outlier: 3.751A pdb=" N ALA F 342 " --> pdb=" O TYR F 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 35 removed outlier: 3.689A pdb=" N PHE G 24 " --> pdb=" O MET G 20 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 63 No H-bonds generated for 'chain 'G' and resid 60 through 63' Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.719A pdb=" N ALA G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 85 Processing helix chain 'G' and resid 90 through 95 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.642A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix Processing helix chain 'G' and resid 125 through 137 removed outlier: 3.770A pdb=" N MET G 131 " --> pdb=" O GLN G 127 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN G 134 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG G 136 " --> pdb=" O ALA G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 258 No H-bonds generated for 'chain 'G' and resid 256 through 258' Processing helix chain 'G' and resid 272 through 279 removed outlier: 4.081A pdb=" N LYS G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE G 279 " --> pdb=" O MET G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 296 removed outlier: 3.625A pdb=" N MET G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE G 296 " --> pdb=" O ALA G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 324 removed outlier: 3.844A pdb=" N PHE G 315 " --> pdb=" O THR G 311 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 316 " --> pdb=" O GLY G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 333 removed outlier: 3.761A pdb=" N TYR G 333 " --> pdb=" O LEU G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 340 No H-bonds generated for 'chain 'G' and resid 337 through 340' Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.060A pdb=" N PHE G 348 " --> pdb=" O PRO G 344 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 352 " --> pdb=" O PHE G 348 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 24 through 26 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.482A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.719A pdb=" N VAL A 22 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LYS A 11 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N GLU A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 59 through 62 removed outlier: 5.840A pdb=" N VAL B 22 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 32 through 35 removed outlier: 7.062A pdb=" N ARG B 206 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N LEU B 35 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N TYR B 208 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.693A pdb=" N LYS B 11 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 19 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N TYR B 13 " --> pdb=" O ARG B 17 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 189 hydrogen bonds defined for protein. 522 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: 1.71 Time building geometry restraints manager: 3.43 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: 2410 1.34 - 1.46: 1355 1.46 - 1.57: 4099 1.57 - 1.69: 7 1.69 - 1.81: 82 Bond restraints: 7953 Sorted by residual: bond pdb=" C7 JSG F 402 " pdb=" N2 JSG F 402 " ideal model delta sigma weight residual 1.621 1.340 0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" CDO JSG F 402 " pdb=" NAO JSG F 402 " ideal model delta sigma weight residual 1.505 1.329 0.176 2.00e-02 2.50e+03 7.72e+01 bond pdb=" CAN JSG F 402 " pdb=" CAP JSG F 402 " ideal model delta sigma weight residual 1.419 1.565 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" C2 DCQ F 403 " pdb=" C3 DCQ F 403 " ideal model delta sigma weight residual 1.485 1.375 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" CEE JSG F 402 " pdb=" OAQ JSG F 402 " ideal model delta sigma weight residual 1.469 1.360 0.109 2.00e-02 2.50e+03 2.98e+01 ... (remaining 7948 not shown) Histogram of bond angle deviations from ideal: 96.61 - 105.22: 190 105.22 - 113.84: 4679 113.84 - 122.45: 4887 122.45 - 131.06: 947 131.06 - 139.67: 45 Bond angle restraints: 10748 Sorted by residual: angle pdb=" C3 DCQ G 403 " pdb=" O3 DCQ G 403 " pdb=" C3M DCQ G 403 " ideal model delta sigma weight residual 115.29 139.67 -24.38 3.00e+00 1.11e-01 6.60e+01 angle pdb=" C4 DCQ G 403 " pdb=" O4 DCQ G 403 " pdb=" C4M DCQ G 403 " ideal model delta sigma weight residual 115.20 138.59 -23.39 3.00e+00 1.11e-01 6.08e+01 angle pdb=" CBJ LMN F 401 " pdb=" CBL LMN F 401 " pdb=" CBR LMN F 401 " ideal model delta sigma weight residual 112.20 135.02 -22.82 3.00e+00 1.11e-01 5.78e+01 angle pdb=" C4 DCQ F 403 " pdb=" O4 DCQ F 403 " pdb=" C4M DCQ F 403 " ideal model delta sigma weight residual 115.20 137.60 -22.40 3.00e+00 1.11e-01 5.57e+01 angle pdb=" C3 DCQ F 403 " pdb=" O3 DCQ F 403 " pdb=" C3M DCQ F 403 " ideal model delta sigma weight residual 115.29 137.13 -21.84 3.00e+00 1.11e-01 5.30e+01 ... (remaining 10743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 4540 25.74 - 51.47: 281 51.47 - 77.21: 35 77.21 - 102.94: 16 102.94 - 128.68: 4 Dihedral angle restraints: 4876 sinusoidal: 2125 harmonic: 2751 Sorted by residual: dihedral pdb=" CA GLY B 39 " pdb=" C GLY B 39 " pdb=" N ALA B 40 " pdb=" CA ALA B 40 " ideal model delta harmonic sigma weight residual -180.00 -139.27 -40.73 0 5.00e+00 4.00e-02 6.64e+01 dihedral pdb=" CA ALA B 40 " pdb=" C ALA B 40 " pdb=" N GLY B 41 " pdb=" CA GLY B 41 " ideal model delta harmonic sigma weight residual 180.00 146.96 33.04 0 5.00e+00 4.00e-02 4.37e+01 dihedral pdb=" CA TYR A 234 " pdb=" C TYR A 234 " pdb=" N LEU A 235 " pdb=" CA LEU A 235 " ideal model delta harmonic sigma weight residual -180.00 -148.85 -31.15 0 5.00e+00 4.00e-02 3.88e+01 ... (remaining 4873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.000: 1277 1.000 - 2.001: 2 2.001 - 3.001: 0 3.001 - 4.001: 0 4.001 - 5.002: 1 Chirality restraints: 1280 Sorted by residual: chirality pdb=" CCB JSG F 402 " pdb=" CCC JSG F 402 " pdb=" OBF JSG F 402 " pdb=" OCL JSG F 402 " both_signs ideal model delta sigma weight residual False 2.42 -2.59 5.00 2.00e-01 2.50e+01 6.25e+02 chirality pdb=" CBG JSG F 402 " pdb=" CBE JSG F 402 " pdb=" CBI JSG F 402 " pdb=" OBH JSG F 402 " both_signs ideal model delta sigma weight residual False -2.55 -1.20 -1.35 2.00e-01 2.50e+01 4.53e+01 chirality pdb=" CEW JSG F 402 " pdb=" C8 JSG F 402 " pdb=" CEX JSG F 402 " pdb=" OFJ JSG F 402 " both_signs ideal model delta sigma weight residual False -2.61 -1.58 -1.03 2.00e-01 2.50e+01 2.65e+01 ... (remaining 1277 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CGB JSG F 402 " 0.060 2.00e-02 2.50e+03 3.47e-02 1.21e+01 pdb=" CGC JSG F 402 " -0.016 2.00e-02 2.50e+03 pdb=" OFJ JSG F 402 " -0.020 2.00e-02 2.50e+03 pdb=" OGA JSG F 402 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 DCQ G 403 " 0.002 2.00e-02 2.50e+03 1.99e-02 1.19e+01 pdb=" C1M DCQ G 403 " 0.040 2.00e-02 2.50e+03 pdb=" C2 DCQ G 403 " -0.005 2.00e-02 2.50e+03 pdb=" C3 DCQ G 403 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DCQ G 403 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DCQ G 403 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DCQ G 403 " 0.015 2.00e-02 2.50e+03 pdb=" C7 DCQ G 403 " -0.029 2.00e-02 2.50e+03 pdb=" O2 DCQ G 403 " -0.042 2.00e-02 2.50e+03 pdb=" O3 DCQ G 403 " 0.011 2.00e-02 2.50e+03 pdb=" O4 DCQ G 403 " 0.006 2.00e-02 2.50e+03 pdb=" O5 DCQ G 403 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CFK JSG F 402 " -0.057 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" CFL JSG F 402 " 0.016 2.00e-02 2.50e+03 pdb=" O3 JSG F 402 " 0.017 2.00e-02 2.50e+03 pdb=" OFY JSG F 402 " 0.023 2.00e-02 2.50e+03 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2283 2.82 - 3.34: 6837 3.34 - 3.86: 12228 3.86 - 4.38: 14287 4.38 - 4.90: 24081 Nonbonded interactions: 59716 Sorted by model distance: nonbonded pdb=" O1B LMT F 404 " pdb=" O6' LMT F 404 " model vdw 2.300 2.440 nonbonded pdb=" O SER G 277 " pdb=" OG SER G 277 " model vdw 2.308 2.440 nonbonded pdb=" O SER F 315 " pdb=" OG SER F 315 " model vdw 2.315 2.440 nonbonded pdb=" O SER A 137 " pdb=" OG SER A 137 " model vdw 2.322 2.440 nonbonded pdb=" O SER B 172 " pdb=" OG SER B 172 " model vdw 2.329 2.440 ... (remaining 59711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 239) selection = chain 'B' } 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 group one per residue 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: 0.650 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: 1.710 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 27.160 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.011 0.281 7953 Z= 0.696 Angle : 1.653 24.381 10748 Z= 0.726 Chirality : 0.164 5.002 1280 Planarity : 0.008 0.080 1303 Dihedral : 17.584 128.679 3102 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.95 % Favored : 89.84 % Rotamer: Outliers : 0.12 % Allowed : 10.29 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -6.48 (0.18), residues: 945 helix: -4.56 (0.10), residues: 507 sheet: -3.41 (0.54), residues: 69 loop : -3.82 (0.26), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 119 HIS 0.007 0.002 HIS F 89 PHE 0.026 0.002 PHE G 280 TYR 0.019 0.002 TYR A 234 ARG 0.006 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9323 (m-40) cc_final: 0.8911 (m110) REVERT: A 134 MET cc_start: 0.8346 (mmm) cc_final: 0.7696 (mmm) REVERT: A 196 ASN cc_start: 0.9083 (t0) cc_final: 0.8473 (t0) REVERT: A 233 VAL cc_start: 0.8886 (m) cc_final: 0.8550 (p) REVERT: B 159 ILE cc_start: 0.9609 (mt) cc_final: 0.9385 (tt) REVERT: B 177 LYS cc_start: 0.8589 (mtmt) cc_final: 0.8340 (mtmm) REVERT: B 223 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8278 (mp0) REVERT: F 29 GLN cc_start: 0.8667 (tp40) cc_final: 0.8254 (tp40) REVERT: F 52 LEU cc_start: 0.8836 (tp) cc_final: 0.8601 (tt) REVERT: F 78 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8215 (ttmt) REVERT: F 93 LEU cc_start: 0.8169 (pp) cc_final: 0.7712 (mt) REVERT: F 267 ASN cc_start: 0.7893 (m-40) cc_final: 0.7660 (m110) REVERT: G 25 MET cc_start: 0.8008 (mmt) cc_final: 0.7779 (tmm) REVERT: G 107 MET cc_start: 0.9462 (mmt) cc_final: 0.9240 (mmt) REVERT: G 276 TRP cc_start: 0.8897 (t-100) cc_final: 0.8359 (t-100) REVERT: G 323 ASP cc_start: 0.9115 (t70) cc_final: 0.8660 (t0) outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.2338 time to fit residues: 89.1271 Evaluate side-chains 205 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.0470 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 212 GLN F 116 ASN F 127 HIS F 248 GLN F 335 ASN F 346 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7953 Z= 0.200 Angle : 0.815 11.866 10748 Z= 0.385 Chirality : 0.045 0.316 1280 Planarity : 0.006 0.063 1303 Dihedral : 14.476 134.712 1334 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.21 % Allowed : 8.15 % Favored : 91.64 % Rotamer: Outliers : 3.97 % Allowed : 19.08 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.93 (0.22), residues: 945 helix: -3.06 (0.18), residues: 484 sheet: -3.08 (0.56), residues: 69 loop : -3.46 (0.27), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 119 HIS 0.005 0.001 HIS F 89 PHE 0.014 0.001 PHE G 280 TYR 0.014 0.001 TYR G 135 ARG 0.005 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 228 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASN cc_start: 0.9442 (m-40) cc_final: 0.9158 (m110) REVERT: A 134 MET cc_start: 0.8224 (mmm) cc_final: 0.7476 (mmm) REVERT: A 233 VAL cc_start: 0.8947 (m) cc_final: 0.8578 (p) REVERT: B 42 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8908 (ptmt) REVERT: B 97 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7779 (t0) REVERT: F 4 ILE cc_start: 0.9326 (mm) cc_final: 0.9109 (mm) REVERT: F 10 GLU cc_start: 0.8385 (tp30) cc_final: 0.8038 (mm-30) REVERT: F 29 GLN cc_start: 0.8730 (tp40) cc_final: 0.8520 (tp40) REVERT: F 78 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8360 (ttmt) REVERT: F 93 LEU cc_start: 0.7870 (pp) cc_final: 0.7520 (mp) REVERT: F 111 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.8964 (mt) REVERT: F 126 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7676 (mtt90) REVERT: F 278 MET cc_start: 0.8498 (tmm) cc_final: 0.8173 (tmm) REVERT: G 25 MET cc_start: 0.8011 (mmt) cc_final: 0.7696 (tmm) REVERT: G 86 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7806 (mtm180) REVERT: G 276 TRP cc_start: 0.8933 (t-100) cc_final: 0.8301 (t-100) REVERT: G 323 ASP cc_start: 0.9174 (t70) cc_final: 0.8796 (t0) outliers start: 32 outliers final: 22 residues processed: 247 average time/residue: 0.2036 time to fit residues: 67.4714 Evaluate side-chains 233 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 218 HIS Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 0.0370 chunk 67 optimal weight: 0.0770 overall best weight: 1.1618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 214 HIS B 85 GLN B 212 GLN ** F 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN F 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7953 Z= 0.183 Angle : 0.703 9.493 10748 Z= 0.339 Chirality : 0.044 0.323 1280 Planarity : 0.005 0.060 1303 Dihedral : 13.525 131.397 1334 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.57 % Favored : 91.32 % Rotamer: Outliers : 5.82 % Allowed : 20.94 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (0.25), residues: 945 helix: -2.14 (0.22), residues: 474 sheet: -2.89 (0.57), residues: 69 loop : -3.10 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 119 HIS 0.004 0.001 HIS F 89 PHE 0.011 0.001 PHE G 280 TYR 0.010 0.001 TYR B 96 ARG 0.004 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 211 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 MET cc_start: 0.8239 (mmm) cc_final: 0.7454 (mmm) REVERT: A 233 VAL cc_start: 0.8928 (m) cc_final: 0.8561 (p) REVERT: B 105 ILE cc_start: 0.9167 (tp) cc_final: 0.8806 (tp) REVERT: F 10 GLU cc_start: 0.8491 (tp30) cc_final: 0.8240 (mm-30) REVERT: F 20 PHE cc_start: 0.8111 (m-80) cc_final: 0.7489 (t80) REVERT: F 93 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7427 (mp) REVERT: F 117 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8493 (p) REVERT: F 278 MET cc_start: 0.8506 (tmm) cc_final: 0.8132 (tmm) REVERT: G 323 ASP cc_start: 0.9173 (t70) cc_final: 0.8791 (t0) outliers start: 47 outliers final: 32 residues processed: 242 average time/residue: 0.2226 time to fit residues: 72.3424 Evaluate side-chains 233 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 199 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN F 116 ASN F 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7953 Z= 0.202 Angle : 0.695 9.504 10748 Z= 0.336 Chirality : 0.044 0.278 1280 Planarity : 0.005 0.057 1303 Dihedral : 13.318 122.298 1334 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.68 % Favored : 91.22 % Rotamer: Outliers : 5.95 % Allowed : 23.54 % Favored : 70.51 % 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: -3.48 (0.25), residues: 945 helix: -1.70 (0.23), residues: 470 sheet: -2.68 (0.57), residues: 69 loop : -2.93 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 276 HIS 0.005 0.001 HIS F 89 PHE 0.022 0.001 PHE G 280 TYR 0.010 0.001 TYR G 135 ARG 0.003 0.000 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 202 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 43 THR cc_start: 0.9238 (p) cc_final: 0.8801 (t) REVERT: A 59 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: A 100 MET cc_start: 0.9036 (tpp) cc_final: 0.8651 (tpp) REVERT: A 134 MET cc_start: 0.8265 (mmm) cc_final: 0.7470 (mmm) REVERT: A 233 VAL cc_start: 0.8896 (m) cc_final: 0.8500 (p) REVERT: B 196 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8668 (t0) REVERT: F 20 PHE cc_start: 0.8132 (m-80) cc_final: 0.7499 (t80) REVERT: F 93 LEU cc_start: 0.7727 (pp) cc_final: 0.7311 (mp) REVERT: F 346 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8684 (m-40) REVERT: G 62 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8974 (tmtt) REVERT: G 323 ASP cc_start: 0.9177 (t70) cc_final: 0.8850 (t0) outliers start: 48 outliers final: 32 residues processed: 230 average time/residue: 0.1966 time to fit residues: 60.3580 Evaluate side-chains 233 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 298 SER Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 284 SER Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.3980 chunk 51 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.0270 chunk 80 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN A 119 ASN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN F 335 ASN F 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7953 Z= 0.139 Angle : 0.639 9.147 10748 Z= 0.309 Chirality : 0.042 0.234 1280 Planarity : 0.004 0.059 1303 Dihedral : 12.557 111.156 1334 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 4.58 % Allowed : 24.66 % Favored : 70.76 % 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: -3.11 (0.26), residues: 945 helix: -1.25 (0.24), residues: 469 sheet: -2.53 (0.54), residues: 79 loop : -2.92 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 255 HIS 0.002 0.001 HIS F 89 PHE 0.007 0.001 PHE B 239 TYR 0.009 0.001 TYR B 234 ARG 0.003 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 219 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8060 (m-30) cc_final: 0.7808 (m-30) REVERT: A 100 MET cc_start: 0.8951 (tpp) cc_final: 0.8646 (tpp) REVERT: A 134 MET cc_start: 0.8275 (mmm) cc_final: 0.7636 (mmm) REVERT: A 233 VAL cc_start: 0.8852 (m) cc_final: 0.8450 (p) REVERT: B 136 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8654 (pm20) REVERT: B 155 ASN cc_start: 0.9437 (t0) cc_final: 0.9132 (t0) REVERT: B 196 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8495 (t0) REVERT: F 20 PHE cc_start: 0.8217 (m-80) cc_final: 0.7621 (t80) REVERT: F 93 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7220 (mp) REVERT: F 117 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (p) REVERT: F 346 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (m-40) REVERT: G 323 ASP cc_start: 0.9182 (t70) cc_final: 0.8847 (t0) outliers start: 37 outliers final: 22 residues processed: 241 average time/residue: 0.2145 time to fit residues: 69.7623 Evaluate side-chains 231 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 204 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 346 ASN Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 ASN F 335 ASN F 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7953 Z= 0.221 Angle : 0.664 9.295 10748 Z= 0.321 Chirality : 0.044 0.228 1280 Planarity : 0.004 0.055 1303 Dihedral : 12.505 98.428 1334 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.68 % Favored : 91.22 % Rotamer: Outliers : 5.20 % Allowed : 24.91 % Favored : 69.89 % 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: -2.79 (0.27), residues: 945 helix: -1.01 (0.24), residues: 473 sheet: -2.51 (0.54), residues: 79 loop : -2.72 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 276 HIS 0.005 0.001 HIS F 89 PHE 0.018 0.001 PHE G 280 TYR 0.006 0.001 TYR B 82 ARG 0.004 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8083 (m-30) cc_final: 0.7829 (m-30) REVERT: A 59 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8637 (m-40) REVERT: A 119 ASN cc_start: 0.9431 (m110) cc_final: 0.9179 (m110) REVERT: A 134 MET cc_start: 0.8337 (mmm) cc_final: 0.7738 (mmm) REVERT: A 233 VAL cc_start: 0.8881 (m) cc_final: 0.8458 (p) REVERT: B 97 ASP cc_start: 0.8151 (m-30) cc_final: 0.7910 (t0) REVERT: B 136 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8684 (pm20) REVERT: B 155 ASN cc_start: 0.9450 (t0) cc_final: 0.9154 (t0) REVERT: B 171 ILE cc_start: 0.9406 (tp) cc_final: 0.9125 (tp) REVERT: F 20 PHE cc_start: 0.8207 (m-80) cc_final: 0.7592 (t80) REVERT: F 34 ILE cc_start: 0.8803 (tp) cc_final: 0.8520 (mp) REVERT: F 117 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8564 (p) REVERT: G 323 ASP cc_start: 0.9173 (t70) cc_final: 0.8921 (t0) outliers start: 42 outliers final: 29 residues processed: 232 average time/residue: 0.1924 time to fit residues: 59.9702 Evaluate side-chains 231 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 336 LEU Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN B 85 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN F 335 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7953 Z= 0.171 Angle : 0.637 9.179 10748 Z= 0.307 Chirality : 0.042 0.215 1280 Planarity : 0.004 0.054 1303 Dihedral : 12.321 88.262 1334 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.51 % Favored : 92.38 % Rotamer: Outliers : 5.08 % Allowed : 25.53 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.27), residues: 945 helix: -0.78 (0.24), residues: 473 sheet: -2.37 (0.56), residues: 79 loop : -2.63 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 255 HIS 0.004 0.001 HIS F 89 PHE 0.009 0.001 PHE G 280 TYR 0.014 0.001 TYR B 234 ARG 0.004 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 0.852 Fit side-chains revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8073 (m-30) cc_final: 0.7847 (m-30) REVERT: A 59 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8622 (m-40) REVERT: A 100 MET cc_start: 0.9007 (tpp) cc_final: 0.8722 (tpp) REVERT: A 119 ASN cc_start: 0.9440 (m110) cc_final: 0.9190 (m110) REVERT: A 134 MET cc_start: 0.8306 (mmm) cc_final: 0.7678 (mmm) REVERT: A 233 VAL cc_start: 0.8873 (m) cc_final: 0.8444 (p) REVERT: B 97 ASP cc_start: 0.8112 (m-30) cc_final: 0.7855 (t0) REVERT: B 134 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7434 (mmm) REVERT: B 136 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8646 (pm20) REVERT: B 155 ASN cc_start: 0.9441 (t0) cc_final: 0.9115 (t0) REVERT: B 171 ILE cc_start: 0.9401 (tp) cc_final: 0.9124 (tp) REVERT: F 20 PHE cc_start: 0.8221 (m-80) cc_final: 0.7620 (t80) REVERT: F 34 ILE cc_start: 0.8757 (tp) cc_final: 0.8513 (mp) REVERT: F 117 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8573 (p) REVERT: F 278 MET cc_start: 0.8564 (ttp) cc_final: 0.8278 (tmm) REVERT: G 62 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8915 (tmtt) REVERT: G 323 ASP cc_start: 0.9186 (t70) cc_final: 0.8896 (t0) outliers start: 41 outliers final: 28 residues processed: 229 average time/residue: 0.1912 time to fit residues: 58.7169 Evaluate side-chains 234 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 279 ILE Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7953 Z= 0.194 Angle : 0.650 11.706 10748 Z= 0.312 Chirality : 0.043 0.211 1280 Planarity : 0.004 0.053 1303 Dihedral : 12.306 85.923 1334 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.15 % Favored : 91.75 % Rotamer: Outliers : 5.20 % Allowed : 25.65 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.27), residues: 945 helix: -0.62 (0.24), residues: 467 sheet: -2.34 (0.57), residues: 79 loop : -2.48 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 276 HIS 0.005 0.001 HIS F 89 PHE 0.019 0.001 PHE G 280 TYR 0.012 0.001 TYR B 234 ARG 0.004 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8068 (m-30) cc_final: 0.7845 (m-30) REVERT: A 100 MET cc_start: 0.8971 (tpp) cc_final: 0.8689 (tpp) REVERT: A 119 ASN cc_start: 0.9434 (m110) cc_final: 0.9195 (m110) REVERT: A 134 MET cc_start: 0.8330 (mmm) cc_final: 0.7793 (mmm) REVERT: A 233 VAL cc_start: 0.8871 (m) cc_final: 0.8458 (p) REVERT: B 127 ILE cc_start: 0.8422 (mm) cc_final: 0.8168 (mm) REVERT: B 134 MET cc_start: 0.7781 (tpp) cc_final: 0.7480 (mmm) REVERT: B 136 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: B 155 ASN cc_start: 0.9442 (t0) cc_final: 0.9123 (t0) REVERT: F 20 PHE cc_start: 0.8218 (m-80) cc_final: 0.7619 (t80) REVERT: F 34 ILE cc_start: 0.8752 (tp) cc_final: 0.8539 (mp) REVERT: F 117 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8591 (p) REVERT: G 62 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8908 (tmtt) REVERT: G 140 MET cc_start: 0.8258 (tmm) cc_final: 0.7988 (tmm) REVERT: G 323 ASP cc_start: 0.9169 (t70) cc_final: 0.8915 (t0) outliers start: 42 outliers final: 32 residues processed: 230 average time/residue: 0.2105 time to fit residues: 64.4233 Evaluate side-chains 237 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7953 Z= 0.243 Angle : 0.678 9.972 10748 Z= 0.325 Chirality : 0.044 0.215 1280 Planarity : 0.004 0.053 1303 Dihedral : 12.357 84.694 1334 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.99 % Favored : 90.90 % Rotamer: Outliers : 4.71 % Allowed : 27.26 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 945 helix: -0.56 (0.24), residues: 473 sheet: -2.40 (0.56), residues: 79 loop : -2.37 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 255 HIS 0.006 0.001 HIS F 89 PHE 0.012 0.001 PHE G 280 TYR 0.011 0.001 TYR A 234 ARG 0.004 0.000 ARG F 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 201 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8067 (m-30) cc_final: 0.7850 (m-30) REVERT: A 43 THR cc_start: 0.9188 (p) cc_final: 0.8807 (m) REVERT: A 100 MET cc_start: 0.8907 (tpp) cc_final: 0.8681 (tpp) REVERT: A 119 ASN cc_start: 0.9426 (m110) cc_final: 0.9176 (m110) REVERT: A 134 MET cc_start: 0.8326 (mmm) cc_final: 0.7716 (mmm) REVERT: A 233 VAL cc_start: 0.8880 (m) cc_final: 0.8435 (p) REVERT: B 127 ILE cc_start: 0.8469 (mm) cc_final: 0.8168 (mm) REVERT: B 134 MET cc_start: 0.7808 (tpp) cc_final: 0.7578 (mmm) REVERT: B 136 GLN cc_start: 0.8977 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: B 155 ASN cc_start: 0.9469 (t0) cc_final: 0.9162 (t0) REVERT: B 171 ILE cc_start: 0.9419 (tp) cc_final: 0.9116 (tp) REVERT: B 196 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8646 (t0) REVERT: F 6 TYR cc_start: 0.8831 (t80) cc_final: 0.8509 (t80) REVERT: F 10 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8304 (mm-30) REVERT: F 20 PHE cc_start: 0.8224 (m-80) cc_final: 0.7586 (t80) REVERT: F 34 ILE cc_start: 0.8885 (tp) cc_final: 0.8667 (mp) REVERT: F 117 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8633 (p) REVERT: G 62 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9027 (tmtt) REVERT: G 140 MET cc_start: 0.8276 (tmm) cc_final: 0.7995 (tmm) REVERT: G 323 ASP cc_start: 0.9191 (t70) cc_final: 0.8893 (t0) outliers start: 38 outliers final: 32 residues processed: 223 average time/residue: 0.1969 time to fit residues: 58.7670 Evaluate side-chains 232 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 196 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 335 ASN Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7953 Z= 0.179 Angle : 0.650 9.369 10748 Z= 0.312 Chirality : 0.042 0.200 1280 Planarity : 0.004 0.052 1303 Dihedral : 12.106 83.864 1334 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.94 % Favored : 91.96 % Rotamer: Outliers : 4.96 % Allowed : 27.26 % Favored : 67.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 945 helix: -0.44 (0.24), residues: 472 sheet: -2.31 (0.57), residues: 79 loop : -2.37 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 255 HIS 0.005 0.001 HIS F 89 PHE 0.017 0.001 PHE G 280 TYR 0.014 0.001 TYR A 234 ARG 0.004 0.000 ARG F 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 204 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ASP cc_start: 0.8045 (m-30) cc_final: 0.7819 (m-30) REVERT: A 119 ASN cc_start: 0.9424 (m110) cc_final: 0.9179 (m110) REVERT: A 134 MET cc_start: 0.8285 (mmm) cc_final: 0.7698 (mmm) REVERT: A 233 VAL cc_start: 0.8854 (m) cc_final: 0.8395 (p) REVERT: B 127 ILE cc_start: 0.8443 (mm) cc_final: 0.8135 (mm) REVERT: B 134 MET cc_start: 0.7828 (tpp) cc_final: 0.7590 (mmm) REVERT: B 136 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: B 155 ASN cc_start: 0.9455 (t0) cc_final: 0.9127 (t0) REVERT: B 171 ILE cc_start: 0.9381 (tp) cc_final: 0.9069 (tp) REVERT: B 196 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8648 (t0) REVERT: F 10 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8229 (mm-30) REVERT: F 20 PHE cc_start: 0.8199 (m-80) cc_final: 0.7628 (t80) REVERT: F 34 ILE cc_start: 0.8869 (tp) cc_final: 0.8659 (mp) REVERT: F 117 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8635 (p) REVERT: G 62 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8960 (tmtt) REVERT: G 140 MET cc_start: 0.8258 (tmm) cc_final: 0.7993 (tmm) REVERT: G 323 ASP cc_start: 0.9169 (t70) cc_final: 0.8902 (t0) outliers start: 40 outliers final: 30 residues processed: 227 average time/residue: 0.2226 time to fit residues: 67.1965 Evaluate side-chains 237 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 203 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASN Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 195 HIS Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 7 LYS Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 136 GLN Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 282 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain G residue 62 LYS Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103703 restraints weight = 12485.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107161 restraints weight = 6824.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.109420 restraints weight = 4537.616| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7953 Z= 0.169 Angle : 0.651 8.926 10748 Z= 0.312 Chirality : 0.042 0.185 1280 Planarity : 0.004 0.052 1303 Dihedral : 11.859 81.743 1334 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.68 % Favored : 91.22 % Rotamer: Outliers : 4.46 % Allowed : 27.88 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.28), residues: 945 helix: -0.31 (0.25), residues: 467 sheet: -2.27 (0.57), residues: 79 loop : -2.29 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 255 HIS 0.004 0.001 HIS F 89 PHE 0.008 0.001 PHE G 280 TYR 0.021 0.001 TYR A 96 ARG 0.004 0.000 ARG F 33 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1956.75 seconds wall clock time: 36 minutes 10.14 seconds (2170.14 seconds total)