Starting phenix.real_space_refine on Thu Mar 14 13:20:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfy_37208/03_2024/8kfy_37208_updated.pdb" } resolution = 3.06 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5754 2.51 5 N 1505 2.21 5 O 1667 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8992 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2342 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 5, 'TRANS': 282} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'OXF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.58 Number of scatterers: 8992 At special positions: 0 Unit cell: (94.64, 120.64, 128.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1667 8.00 N 1505 7.00 C 5754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 1.8 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.5% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 211 No H-bonds generated for 'chain 'A' and resid 208 through 211' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 227 through 230 removed outlier: 3.692A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 230' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.790A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.702A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'R' and resid 31 through 61 Processing helix chain 'R' and resid 69 through 96 removed outlier: 3.913A pdb=" N SER R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Proline residue: R 89 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.831A pdb=" N LYS R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 171 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 190 through 204 removed outlier: 3.978A pdb=" N LYS R 193 " --> pdb=" O GLN R 190 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE R 200 " --> pdb=" O PHE R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 226 removed outlier: 3.637A pdb=" N ILE R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 265 Proline residue: R 253 - end of helix Processing helix chain 'R' and resid 272 through 300 removed outlier: 4.136A pdb=" N HIS R 292 " --> pdb=" O ILE R 288 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N CYS R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N CYS R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 305 through 316 Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 209 through 211 No H-bonds generated for 'chain 'S' and resid 209 through 211' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.621A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.761A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.241A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.783A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 221 through 223 removed outlier: 4.356A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.572A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.638A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 172 through 177 Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.616A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.316A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 143 through 148 432 hydrogen bonds defined for protein. 1218 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: 2.69 Time building geometry restraints manager: 3.78 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: 2856 1.34 - 1.46: 2115 1.46 - 1.58: 4116 1.58 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 9182 Sorted by residual: bond pdb=" CA TYR S 161 " pdb=" CB TYR S 161 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.47e-02 4.63e+03 3.61e+00 bond pdb=" C7 OXF R 601 " pdb=" C8 OXF R 601 " ideal model delta sigma weight residual 1.528 1.495 0.033 2.00e-02 2.50e+03 2.70e+00 bond pdb=" SD MET R 105 " pdb=" CE MET R 105 " ideal model delta sigma weight residual 1.791 1.758 0.033 2.50e-02 1.60e+03 1.72e+00 bond pdb=" C7 OXF R 601 " pdb=" O1 OXF R 601 " ideal model delta sigma weight residual 1.399 1.423 -0.024 2.00e-02 2.50e+03 1.39e+00 bond pdb=" C MET R 105 " pdb=" O MET R 105 " ideal model delta sigma weight residual 1.237 1.224 0.012 1.17e-02 7.31e+03 1.12e+00 ... (remaining 9177 not shown) Histogram of bond angle deviations from ideal: 98.14 - 105.34: 105 105.34 - 112.55: 4828 112.55 - 119.75: 2957 119.75 - 126.96: 4439 126.96 - 134.16: 96 Bond angle restraints: 12425 Sorted by residual: angle pdb=" C17 OXF R 601 " pdb=" C16 OXF R 601 " pdb=" O3 OXF R 601 " ideal model delta sigma weight residual 93.18 120.18 -27.00 3.00e+00 1.11e-01 8.10e+01 angle pdb=" C21 OXF R 601 " pdb=" C16 OXF R 601 " pdb=" O3 OXF R 601 " ideal model delta sigma weight residual 140.31 118.49 21.82 3.00e+00 1.11e-01 5.29e+01 angle pdb=" C15 OXF R 601 " pdb=" C10 OXF R 601 " pdb=" C9 OXF R 601 " ideal model delta sigma weight residual 109.62 120.91 -11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" C12 OXF R 601 " pdb=" O3 OXF R 601 " pdb=" C16 OXF R 601 " ideal model delta sigma weight residual 109.47 119.89 -10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" CB MET R 105 " pdb=" CG MET R 105 " pdb=" SD MET R 105 " ideal model delta sigma weight residual 112.70 122.76 -10.06 3.00e+00 1.11e-01 1.13e+01 ... (remaining 12420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4710 17.68 - 35.37: 558 35.37 - 53.05: 146 53.05 - 70.73: 16 70.73 - 88.42: 5 Dihedral angle restraints: 5435 sinusoidal: 2121 harmonic: 3314 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N THR R 291 " pdb=" CA THR R 291 " ideal model delta harmonic sigma weight residual 180.00 148.76 31.24 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG S 179 " pdb=" C ARG S 179 " pdb=" N MET S 180 " pdb=" CA MET S 180 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA GLN S 130 " pdb=" C GLN S 130 " pdb=" N ALA S 131 " pdb=" CA ALA S 131 " ideal model delta harmonic sigma weight residual -180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 969 0.036 - 0.071: 318 0.071 - 0.107: 102 0.107 - 0.142: 20 0.142 - 0.178: 5 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CA PHE R 290 " pdb=" N PHE R 290 " pdb=" C PHE R 290 " pdb=" CB PHE R 290 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CB VAL R 109 " pdb=" CA VAL R 109 " pdb=" CG1 VAL R 109 " pdb=" CG2 VAL R 109 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB THR R 291 " pdb=" CA THR R 291 " pdb=" OG1 THR R 291 " pdb=" CG2 THR R 291 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 1411 not shown) Planarity restraints: 1556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO B 236 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO S 224 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET R 105 " 0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" C MET R 105 " -0.035 2.00e-02 2.50e+03 pdb=" O MET R 105 " 0.013 2.00e-02 2.50e+03 pdb=" N CYS R 106 " 0.012 2.00e-02 2.50e+03 ... (remaining 1553 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 254 2.70 - 3.25: 8884 3.25 - 3.80: 14835 3.80 - 4.35: 19195 4.35 - 4.90: 32222 Nonbonded interactions: 75390 Sorted by model distance: nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.155 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.182 2.440 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.187 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.249 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.269 2.440 ... (remaining 75385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.000 Extract box with map and model: 3.830 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9182 Z= 0.228 Angle : 0.641 27.005 12425 Z= 0.322 Chirality : 0.041 0.178 1414 Planarity : 0.004 0.058 1556 Dihedral : 15.908 88.418 3288 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.20 % Allowed : 25.61 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.35 (0.25), residues: 1125 helix: 2.52 (0.26), residues: 398 sheet: 0.62 (0.30), residues: 288 loop : -0.42 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.003 0.001 HIS R 292 PHE 0.021 0.001 PHE R 84 TYR 0.014 0.001 TYR B 85 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7448 (mpp) cc_final: 0.7088 (mmm) REVERT: A 349 LYS cc_start: 0.7793 (mtmm) cc_final: 0.7578 (mtmm) REVERT: B 19 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7122 (mtm-85) REVERT: R 46 PHE cc_start: 0.8327 (t80) cc_final: 0.8052 (t80) REVERT: R 202 MET cc_start: 0.7523 (mmm) cc_final: 0.7200 (mtp) REVERT: S 154 LEU cc_start: 0.8196 (tp) cc_final: 0.7943 (tp) outliers start: 2 outliers final: 1 residues processed: 227 average time/residue: 0.2665 time to fit residues: 78.0310 Evaluate side-chains 223 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9182 Z= 0.202 Angle : 0.496 8.966 12425 Z= 0.270 Chirality : 0.041 0.181 1414 Planarity : 0.004 0.057 1556 Dihedral : 5.349 75.526 1240 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.74 % Allowed : 22.37 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.42 (0.25), residues: 1125 helix: 2.62 (0.26), residues: 399 sheet: 0.59 (0.30), residues: 286 loop : -0.37 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 297 HIS 0.005 0.001 HIS S 155 PHE 0.022 0.001 PHE R 214 TYR 0.011 0.001 TYR R 187 ARG 0.003 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7418 (mpp) cc_final: 0.7131 (mmm) REVERT: A 184 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 298 GLU cc_start: 0.6545 (tp30) cc_final: 0.6235 (tp30) REVERT: B 19 ARG cc_start: 0.7312 (mtm-85) cc_final: 0.6973 (mtm-85) REVERT: B 263 THR cc_start: 0.8191 (p) cc_final: 0.7852 (m) REVERT: B 301 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7953 (mtpp) REVERT: R 46 PHE cc_start: 0.8338 (t80) cc_final: 0.8095 (t80) REVERT: R 124 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8171 (mm) REVERT: R 202 MET cc_start: 0.7568 (mmm) cc_final: 0.7208 (mtp) REVERT: R 215 MET cc_start: 0.8076 (mmm) cc_final: 0.7612 (mpp) REVERT: R 250 PHE cc_start: 0.7113 (m-10) cc_final: 0.6909 (m-10) REVERT: R 257 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.8141 (p) REVERT: S 154 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7817 (tp) REVERT: S 160 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8404 (m) outliers start: 37 outliers final: 23 residues processed: 232 average time/residue: 0.2396 time to fit residues: 73.4464 Evaluate side-chains 238 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9182 Z= 0.253 Angle : 0.498 7.692 12425 Z= 0.270 Chirality : 0.041 0.209 1414 Planarity : 0.004 0.056 1556 Dihedral : 5.409 76.826 1240 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.45 % Allowed : 21.76 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.29 (0.25), residues: 1125 helix: 2.55 (0.25), residues: 400 sheet: 0.46 (0.30), residues: 287 loop : -0.44 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.001 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7388 (mpp) cc_final: 0.7109 (mmm) REVERT: A 317 LYS cc_start: 0.8417 (ptpp) cc_final: 0.7778 (ptpp) REVERT: B 19 ARG cc_start: 0.7252 (mtm-85) cc_final: 0.6993 (mtm-85) REVERT: B 134 ARG cc_start: 0.7917 (ttp80) cc_final: 0.7549 (ttp-110) REVERT: B 178 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (p) REVERT: B 197 ARG cc_start: 0.7000 (mpt-90) cc_final: 0.6598 (mpt-90) REVERT: B 263 THR cc_start: 0.8214 (p) cc_final: 0.7844 (m) REVERT: B 301 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7982 (mtpp) REVERT: R 46 PHE cc_start: 0.8392 (t80) cc_final: 0.8150 (t80) REVERT: R 70 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8062 (m) REVERT: R 103 THR cc_start: 0.8108 (p) cc_final: 0.7761 (t) REVERT: R 124 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8197 (mm) REVERT: R 202 MET cc_start: 0.7559 (mmm) cc_final: 0.7180 (mtp) REVERT: R 250 PHE cc_start: 0.7043 (m-10) cc_final: 0.6769 (m-10) REVERT: R 257 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8129 (p) REVERT: S 154 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (tp) REVERT: S 160 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8497 (m) REVERT: S 185 SER cc_start: 0.8386 (m) cc_final: 0.8114 (p) outliers start: 44 outliers final: 26 residues processed: 243 average time/residue: 0.2257 time to fit residues: 73.3660 Evaluate side-chains 257 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 224 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.0670 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9182 Z= 0.236 Angle : 0.491 7.362 12425 Z= 0.266 Chirality : 0.041 0.186 1414 Planarity : 0.004 0.056 1556 Dihedral : 5.385 77.308 1240 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.06 % Allowed : 22.17 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.21 (0.25), residues: 1125 helix: 2.51 (0.25), residues: 400 sheet: 0.34 (0.29), residues: 290 loop : -0.47 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.022 0.001 PHE R 214 TYR 0.021 0.001 TYR S 223 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 218 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7398 (mpp) cc_final: 0.7115 (mmm) REVERT: A 298 GLU cc_start: 0.6518 (tp30) cc_final: 0.6140 (tp30) REVERT: A 345 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7872 (mptt) REVERT: B 19 ARG cc_start: 0.7240 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: B 197 ARG cc_start: 0.7004 (mpt-90) cc_final: 0.6602 (mpt-90) REVERT: B 251 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8315 (mtt90) REVERT: B 263 THR cc_start: 0.8287 (p) cc_final: 0.7830 (m) REVERT: B 301 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (mtpp) REVERT: R 46 PHE cc_start: 0.8399 (t80) cc_final: 0.8156 (t80) REVERT: R 103 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7805 (t) REVERT: R 124 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8195 (mm) REVERT: R 202 MET cc_start: 0.7541 (mmm) cc_final: 0.7176 (mtp) REVERT: R 250 PHE cc_start: 0.6995 (m-10) cc_final: 0.6756 (m-10) REVERT: R 257 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8094 (p) REVERT: R 278 LEU cc_start: 0.8022 (mm) cc_final: 0.7771 (mt) REVERT: S 154 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7845 (tp) REVERT: S 185 SER cc_start: 0.8387 (m) cc_final: 0.8086 (p) outliers start: 50 outliers final: 29 residues processed: 242 average time/residue: 0.2256 time to fit residues: 72.8392 Evaluate side-chains 250 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 216 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9182 Z= 0.294 Angle : 0.508 7.293 12425 Z= 0.277 Chirality : 0.042 0.197 1414 Planarity : 0.004 0.056 1556 Dihedral : 5.452 76.814 1240 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.55 % Allowed : 22.77 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.06 (0.25), residues: 1125 helix: 2.40 (0.25), residues: 401 sheet: 0.19 (0.29), residues: 294 loop : -0.53 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP S 47 HIS 0.004 0.001 HIS B 91 PHE 0.024 0.002 PHE R 214 TYR 0.022 0.002 TYR S 223 ARG 0.003 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7448 (mpp) cc_final: 0.7123 (mmm) REVERT: A 298 GLU cc_start: 0.6646 (tp30) cc_final: 0.6271 (tp30) REVERT: A 345 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7871 (mptt) REVERT: B 134 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7589 (ttp80) REVERT: B 197 ARG cc_start: 0.7025 (mpt-90) cc_final: 0.6581 (mpt-90) REVERT: B 301 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8009 (mtpp) REVERT: R 46 PHE cc_start: 0.8450 (t80) cc_final: 0.8197 (t80) REVERT: R 103 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7809 (t) REVERT: R 124 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (mm) REVERT: R 183 CYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5786 (t) REVERT: R 202 MET cc_start: 0.7546 (mmm) cc_final: 0.7248 (mtp) REVERT: R 250 PHE cc_start: 0.7064 (m-10) cc_final: 0.6827 (m-10) REVERT: R 257 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8100 (p) REVERT: R 278 LEU cc_start: 0.8218 (mm) cc_final: 0.7943 (mt) REVERT: S 185 SER cc_start: 0.8377 (m) cc_final: 0.8061 (p) outliers start: 45 outliers final: 36 residues processed: 235 average time/residue: 0.2319 time to fit residues: 72.5555 Evaluate side-chains 251 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 210 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 301 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 151 THR Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain R residue 308 LYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.2980 chunk 103 optimal weight: 0.4980 chunk 12 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9182 Z= 0.136 Angle : 0.460 6.818 12425 Z= 0.247 Chirality : 0.039 0.189 1414 Planarity : 0.004 0.056 1556 Dihedral : 5.285 79.773 1240 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.25 % Allowed : 23.28 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.31 (0.25), residues: 1125 helix: 2.65 (0.26), residues: 401 sheet: 0.44 (0.30), residues: 281 loop : -0.50 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 155 PHE 0.019 0.001 PHE A 250 TYR 0.018 0.001 TYR S 223 ARG 0.001 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 214 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.6616 (tp30) cc_final: 0.6229 (tp30) REVERT: A 345 LYS cc_start: 0.8111 (ttpt) cc_final: 0.7865 (mptt) REVERT: B 19 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6912 (mtm-85) REVERT: B 134 ARG cc_start: 0.7861 (ttp80) cc_final: 0.7610 (ttp80) REVERT: B 197 ARG cc_start: 0.7010 (mpt-90) cc_final: 0.6546 (mpt-90) REVERT: B 263 THR cc_start: 0.8162 (p) cc_final: 0.7869 (m) REVERT: B 301 LYS cc_start: 0.8271 (mtpt) cc_final: 0.8020 (mtpp) REVERT: R 46 PHE cc_start: 0.8368 (t80) cc_final: 0.8093 (t80) REVERT: R 83 LEU cc_start: 0.8783 (tt) cc_final: 0.8583 (tp) REVERT: R 103 THR cc_start: 0.8126 (p) cc_final: 0.7783 (t) REVERT: R 124 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mm) REVERT: R 191 THR cc_start: 0.3584 (OUTLIER) cc_final: 0.3330 (m) REVERT: R 202 MET cc_start: 0.7486 (mmm) cc_final: 0.7099 (mtp) REVERT: R 250 PHE cc_start: 0.6917 (m-10) cc_final: 0.6676 (m-10) REVERT: R 257 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8098 (p) REVERT: R 278 LEU cc_start: 0.8079 (mm) cc_final: 0.7816 (mt) REVERT: S 185 SER cc_start: 0.8345 (m) cc_final: 0.8024 (p) outliers start: 42 outliers final: 31 residues processed: 233 average time/residue: 0.2318 time to fit residues: 72.3627 Evaluate side-chains 244 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 210 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.0570 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.178 Angle : 0.465 6.936 12425 Z= 0.251 Chirality : 0.040 0.195 1414 Planarity : 0.004 0.055 1556 Dihedral : 5.257 79.848 1240 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.95 % Allowed : 23.38 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.30 (0.25), residues: 1125 helix: 2.65 (0.25), residues: 401 sheet: 0.43 (0.30), residues: 278 loop : -0.50 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.019 0.001 PHE R 214 TYR 0.021 0.001 TYR S 223 ARG 0.001 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 214 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.8532 (ptpp) cc_final: 0.8083 (ptpp) REVERT: A 345 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7869 (mptt) REVERT: B 134 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7615 (ttp80) REVERT: B 197 ARG cc_start: 0.6996 (mpt-90) cc_final: 0.6522 (mpt-90) REVERT: B 263 THR cc_start: 0.8170 (p) cc_final: 0.7889 (m) REVERT: B 301 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8067 (mtpp) REVERT: R 103 THR cc_start: 0.8166 (p) cc_final: 0.7819 (t) REVERT: R 191 THR cc_start: 0.3620 (OUTLIER) cc_final: 0.3370 (m) REVERT: R 202 MET cc_start: 0.7539 (mmm) cc_final: 0.7155 (mtp) REVERT: R 250 PHE cc_start: 0.6910 (m-10) cc_final: 0.6669 (m-10) REVERT: R 256 VAL cc_start: 0.8006 (t) cc_final: 0.7762 (p) REVERT: R 257 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8089 (p) REVERT: R 278 LEU cc_start: 0.8188 (mm) cc_final: 0.7903 (mt) REVERT: S 34 MET cc_start: 0.8250 (mmm) cc_final: 0.8016 (mmm) REVERT: S 185 SER cc_start: 0.8361 (m) cc_final: 0.8052 (p) outliers start: 39 outliers final: 31 residues processed: 233 average time/residue: 0.2269 time to fit residues: 70.4671 Evaluate side-chains 245 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 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 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.220 Angle : 0.478 6.971 12425 Z= 0.258 Chirality : 0.041 0.197 1414 Planarity : 0.004 0.054 1556 Dihedral : 5.278 79.184 1240 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.85 % Allowed : 23.38 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.27 (0.25), residues: 1125 helix: 2.60 (0.25), residues: 401 sheet: 0.46 (0.30), residues: 286 loop : -0.55 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.003 0.001 HIS B 91 PHE 0.021 0.001 PHE R 214 TYR 0.022 0.001 TYR S 223 ARG 0.002 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 216 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.6647 (tp30) cc_final: 0.6245 (tp30) REVERT: A 345 LYS cc_start: 0.8125 (ttpt) cc_final: 0.7871 (mptt) REVERT: B 134 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7589 (ttp80) REVERT: B 197 ARG cc_start: 0.7018 (mpt-90) cc_final: 0.6561 (mpt-90) REVERT: B 263 THR cc_start: 0.8185 (p) cc_final: 0.7907 (m) REVERT: B 301 LYS cc_start: 0.8323 (mtpt) cc_final: 0.8066 (mtpp) REVERT: R 46 PHE cc_start: 0.8394 (t80) cc_final: 0.8103 (t80) REVERT: R 103 THR cc_start: 0.8142 (p) cc_final: 0.7807 (t) REVERT: R 191 THR cc_start: 0.3637 (OUTLIER) cc_final: 0.3386 (m) REVERT: R 202 MET cc_start: 0.7535 (mmm) cc_final: 0.7161 (mtp) REVERT: R 208 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (mt) REVERT: R 250 PHE cc_start: 0.6930 (m-10) cc_final: 0.6710 (m-10) REVERT: R 256 VAL cc_start: 0.8008 (t) cc_final: 0.7759 (p) REVERT: R 257 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8078 (p) REVERT: R 278 LEU cc_start: 0.8207 (mm) cc_final: 0.7924 (mt) REVERT: S 78 THR cc_start: 0.8264 (t) cc_final: 0.8008 (p) REVERT: S 185 SER cc_start: 0.8356 (m) cc_final: 0.8062 (p) outliers start: 38 outliers final: 33 residues processed: 234 average time/residue: 0.2355 time to fit residues: 73.4780 Evaluate side-chains 248 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 212 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 182 ASN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.0010 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.190 Angle : 0.469 6.850 12425 Z= 0.254 Chirality : 0.040 0.195 1414 Planarity : 0.004 0.056 1556 Dihedral : 5.250 79.307 1240 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.74 % Allowed : 23.68 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.27 (0.25), residues: 1125 helix: 2.62 (0.25), residues: 401 sheet: 0.44 (0.30), residues: 278 loop : -0.53 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.001 PHE R 214 TYR 0.020 0.001 TYR S 223 ARG 0.002 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 210 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.6658 (tp30) cc_final: 0.6254 (tp30) REVERT: A 317 LYS cc_start: 0.8533 (ptpp) cc_final: 0.8246 (ptpt) REVERT: A 345 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7867 (mptt) REVERT: B 134 ARG cc_start: 0.7847 (ttp80) cc_final: 0.7600 (ttp80) REVERT: B 197 ARG cc_start: 0.7040 (mpt-90) cc_final: 0.6538 (mpt-90) REVERT: B 263 THR cc_start: 0.8186 (p) cc_final: 0.7900 (m) REVERT: B 301 LYS cc_start: 0.8332 (mtpt) cc_final: 0.8102 (mtpp) REVERT: R 46 PHE cc_start: 0.8393 (t80) cc_final: 0.8086 (t80) REVERT: R 103 THR cc_start: 0.8159 (p) cc_final: 0.7826 (t) REVERT: R 191 THR cc_start: 0.3545 (OUTLIER) cc_final: 0.3288 (m) REVERT: R 202 MET cc_start: 0.7524 (mmm) cc_final: 0.7144 (mtp) REVERT: R 250 PHE cc_start: 0.6914 (m-10) cc_final: 0.6670 (m-10) REVERT: R 257 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8096 (p) REVERT: R 278 LEU cc_start: 0.8201 (mm) cc_final: 0.7910 (mt) REVERT: S 78 THR cc_start: 0.8261 (t) cc_final: 0.8009 (p) REVERT: S 185 SER cc_start: 0.8355 (m) cc_final: 0.8058 (p) outliers start: 37 outliers final: 31 residues processed: 226 average time/residue: 0.2358 time to fit residues: 70.5570 Evaluate side-chains 243 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET 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: 0.0270 chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9182 Z= 0.162 Angle : 0.463 6.768 12425 Z= 0.250 Chirality : 0.040 0.202 1414 Planarity : 0.004 0.053 1556 Dihedral : 5.189 79.746 1240 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.64 % Allowed : 23.79 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.35 (0.25), residues: 1125 helix: 2.66 (0.26), residues: 401 sheet: 0.52 (0.30), residues: 281 loop : -0.49 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS R 292 PHE 0.017 0.001 PHE R 214 TYR 0.011 0.001 TYR S 223 ARG 0.001 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 THR cc_start: 0.8315 (m) cc_final: 0.8089 (m) REVERT: A 298 GLU cc_start: 0.6645 (tp30) cc_final: 0.6237 (tp30) REVERT: A 317 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8217 (ptpt) REVERT: A 345 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7862 (mptt) REVERT: B 134 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7609 (ttp80) REVERT: B 197 ARG cc_start: 0.7044 (mpt-90) cc_final: 0.6513 (mpt-90) REVERT: B 263 THR cc_start: 0.8195 (p) cc_final: 0.7887 (m) REVERT: R 46 PHE cc_start: 0.8393 (t80) cc_final: 0.8065 (t80) REVERT: R 103 THR cc_start: 0.8129 (p) cc_final: 0.7793 (t) REVERT: R 191 THR cc_start: 0.3375 (OUTLIER) cc_final: 0.3123 (m) REVERT: R 202 MET cc_start: 0.7529 (mmm) cc_final: 0.7287 (mtp) REVERT: R 250 PHE cc_start: 0.6914 (m-10) cc_final: 0.6680 (m-10) REVERT: R 257 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (p) REVERT: R 278 LEU cc_start: 0.8192 (mm) cc_final: 0.7814 (mt) REVERT: S 78 THR cc_start: 0.8250 (t) cc_final: 0.7996 (p) REVERT: S 185 SER cc_start: 0.8351 (m) cc_final: 0.8061 (p) outliers start: 36 outliers final: 31 residues processed: 232 average time/residue: 0.2363 time to fit residues: 73.2588 Evaluate side-chains 245 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 35 LYS Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain R residue 61 VAL Chi-restraints excluded: chain R residue 83 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 143 LYS Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 191 THR Chi-restraints excluded: chain R residue 226 LYS Chi-restraints excluded: chain R residue 257 VAL Chi-restraints excluded: chain R residue 294 CYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 180 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.131317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111332 restraints weight = 13610.590| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.18 r_work: 0.3306 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9182 Z= 0.193 Angle : 0.473 6.752 12425 Z= 0.255 Chirality : 0.040 0.202 1414 Planarity : 0.004 0.055 1556 Dihedral : 5.203 78.460 1240 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.34 % Allowed : 23.99 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.32 (0.25), residues: 1125 helix: 2.65 (0.26), residues: 400 sheet: 0.51 (0.30), residues: 286 loop : -0.55 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE R 214 TYR 0.013 0.001 TYR S 223 ARG 0.002 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2534.27 seconds wall clock time: 46 minutes 0.52 seconds (2760.52 seconds total)