Starting phenix.real_space_refine on Wed Feb 14 06:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gut_34279/02_2024/8gut_34279_neut_updated.pdb" } resolution = 2.98 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 66 5.16 5 C 5611 2.51 5 N 1498 2.21 5 O 1624 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8800 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1725 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 2} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2250 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1760 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'KO8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.27, per 1000 atoms: 0.60 Number of scatterers: 8800 At special positions: 0 Unit cell: (89.6, 116.48, 131.84, 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 66 16.00 F 1 9.00 O 1624 8.00 N 1498 7.00 C 5611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 179 " 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 15 sheets defined 35.2% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.512A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 227 through 231' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.409A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 350 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 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.560A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'R' and resid 22 through 24 No H-bonds generated for 'chain 'R' and resid 22 through 24' Processing helix chain 'R' and resid 33 through 60 removed outlier: 3.533A pdb=" N ALA R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL R 38 " --> pdb=" O THR R 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 94 Processing helix chain 'R' and resid 103 through 136 removed outlier: 3.726A pdb=" N LEU R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS R 109 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 170 Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 188 through 225 Processing helix chain 'R' and resid 238 through 270 removed outlier: 3.705A pdb=" N LEU R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Proline residue: R 260 - end of helix removed outlier: 3.814A pdb=" N ALA R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 299 removed outlier: 3.684A pdb=" N ASN R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER R 292 " --> pdb=" O CYS R 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 304 through 318 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 220 through 226 removed outlier: 6.796A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.801A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.736A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.573A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.879A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.547A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.520A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.731A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) 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 95 through 97 removed outlier: 3.676A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 92 through 94 Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.190A pdb=" N LYS S 232 " --> pdb=" O VAL S 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'S' and resid 143 through 148 Processing sheet with id= O, first strand: chain 'S' and resid 214 through 219 removed outlier: 3.710A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1143 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.56 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.44: 2486 1.44 - 1.56: 4997 1.56 - 1.69: 2 1.69 - 1.82: 95 Bond restraints: 8988 Sorted by residual: bond pdb=" C11 KO8 R 401 " pdb=" N2 KO8 R 401 " ideal model delta sigma weight residual 1.477 1.353 0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C11 KO8 R 401 " pdb=" N1 KO8 R 401 " ideal model delta sigma weight residual 1.476 1.384 0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C10 KO8 R 401 " pdb=" N2 KO8 R 401 " ideal model delta sigma weight residual 1.444 1.360 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" C23 KO8 R 401 " pdb=" O3 KO8 R 401 " ideal model delta sigma weight residual 1.478 1.397 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C21 KO8 R 401 " pdb=" N4 KO8 R 401 " ideal model delta sigma weight residual 1.527 1.453 0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 8983 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.66: 135 105.66 - 112.74: 4853 112.74 - 119.82: 2848 119.82 - 126.89: 4228 126.89 - 133.97: 114 Bond angle restraints: 12178 Sorted by residual: angle pdb=" CA PRO R 184 " pdb=" N PRO R 184 " pdb=" CD PRO R 184 " ideal model delta sigma weight residual 112.00 104.55 7.45 1.40e+00 5.10e-01 2.83e+01 angle pdb=" CB LYS C 20 " pdb=" CG LYS C 20 " pdb=" CD LYS C 20 " ideal model delta sigma weight residual 111.30 119.89 -8.59 2.30e+00 1.89e-01 1.40e+01 angle pdb=" CA ARG B 129 " pdb=" CB ARG B 129 " pdb=" CG ARG B 129 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.46 126.47 -4.01 1.41e+00 5.03e-01 8.09e+00 angle pdb=" N PRO R 184 " pdb=" CD PRO R 184 " pdb=" CG PRO R 184 " ideal model delta sigma weight residual 103.20 98.99 4.21 1.50e+00 4.44e-01 7.89e+00 ... (remaining 12173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.36: 4955 28.36 - 56.71: 342 56.71 - 85.07: 17 85.07 - 113.42: 2 113.42 - 141.78: 1 Dihedral angle restraints: 5317 sinusoidal: 2033 harmonic: 3284 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 134.89 -41.89 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" N3 KO8 R 401 " pdb=" C19 KO8 R 401 " pdb=" C20 KO8 R 401 " pdb=" N4 KO8 R 401 " ideal model delta sinusoidal sigma weight residual -137.77 4.01 -141.78 1 3.00e+01 1.11e-03 1.90e+01 dihedral pdb=" CA ARG B 219 " pdb=" C ARG B 219 " pdb=" N GLN B 220 " pdb=" CA GLN B 220 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 971 0.037 - 0.074: 298 0.074 - 0.111: 97 0.111 - 0.148: 22 0.148 - 0.185: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB THR R 116 " pdb=" CA THR R 116 " pdb=" OG1 THR R 116 " pdb=" CG2 THR R 116 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" C21 KO8 R 401 " pdb=" C22 KO8 R 401 " pdb=" C25 KO8 R 401 " pdb=" N4 KO8 R 401 " both_signs ideal model delta sigma weight residual False -2.52 -2.65 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1386 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE R 183 " 0.077 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO R 184 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO R 184 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO R 184 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.042 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO B 39 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 67 " -0.029 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO R 68 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 68 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 68 " -0.025 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 306 2.71 - 3.26: 8766 3.26 - 3.80: 14980 3.80 - 4.35: 18307 4.35 - 4.90: 31261 Nonbonded interactions: 73620 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG SER S 52 " model vdw 2.206 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.207 2.440 nonbonded pdb=" O SER R 161 " pdb=" OG SER R 165 " model vdw 2.207 2.440 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.228 2.440 ... (remaining 73615 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.340 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.810 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:13.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.004 0.124 8988 Z= 0.288 Angle : 0.575 8.591 12178 Z= 0.295 Chirality : 0.041 0.185 1389 Planarity : 0.005 0.113 1526 Dihedral : 17.280 141.778 3190 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 31.92 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.25), residues: 1117 helix: 1.13 (0.26), residues: 414 sheet: -0.79 (0.31), residues: 275 loop : -1.12 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.001 HIS R 62 PHE 0.012 0.001 PHE A 191 TYR 0.013 0.001 TYR R 190 ARG 0.009 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 22 ARG cc_start: 0.7328 (mtt180) cc_final: 0.7092 (mtt180) REVERT: B 61 MET cc_start: 0.7929 (ptm) cc_final: 0.7717 (tmm) REVERT: B 120 ILE cc_start: 0.8111 (mm) cc_final: 0.7812 (mp) REVERT: B 197 ARG cc_start: 0.7846 (tpt170) cc_final: 0.7500 (mmp-170) REVERT: B 219 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7454 (ttm110) REVERT: B 270 ILE cc_start: 0.8810 (pt) cc_final: 0.8577 (pp) REVERT: B 275 SER cc_start: 0.8204 (p) cc_final: 0.7849 (p) REVERT: S 57 THR cc_start: 0.8417 (p) cc_final: 0.7940 (t) REVERT: S 159 ASN cc_start: 0.7997 (m-40) cc_final: 0.7586 (m-40) REVERT: S 221 LEU cc_start: 0.8233 (tp) cc_final: 0.7928 (tm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 1.1707 time to fit residues: 271.2306 Evaluate side-chains 199 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.0831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8988 Z= 0.254 Angle : 0.559 8.394 12178 Z= 0.286 Chirality : 0.042 0.137 1389 Planarity : 0.004 0.057 1526 Dihedral : 6.063 136.720 1231 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.29 % Allowed : 29.07 % Favored : 65.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.25), residues: 1117 helix: 1.34 (0.25), residues: 407 sheet: -0.79 (0.30), residues: 292 loop : -1.12 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.011 0.001 PHE B 151 TYR 0.012 0.001 TYR A 230 ARG 0.006 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 211 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7525 (tt0) cc_final: 0.7312 (tt0) REVERT: A 231 ASP cc_start: 0.8492 (m-30) cc_final: 0.8134 (m-30) REVERT: B 67 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8131 (p) REVERT: B 120 ILE cc_start: 0.8041 (mm) cc_final: 0.7697 (mp) REVERT: B 197 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7530 (mmp-170) REVERT: B 212 ASP cc_start: 0.7737 (t0) cc_final: 0.7323 (t0) REVERT: B 270 ILE cc_start: 0.8814 (pt) cc_final: 0.8582 (pp) REVERT: C 13 ARG cc_start: 0.7136 (ptp90) cc_final: 0.6889 (ptp90) REVERT: C 29 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: S 129 THR cc_start: 0.7938 (t) cc_final: 0.7607 (m) REVERT: S 159 ASN cc_start: 0.8069 (m-40) cc_final: 0.7690 (m-40) REVERT: S 221 LEU cc_start: 0.8309 (tp) cc_final: 0.7842 (tm) REVERT: S 222 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6665 (pm20) REVERT: S 226 THR cc_start: 0.8396 (m) cc_final: 0.8128 (t) outliers start: 50 outliers final: 20 residues processed: 242 average time/residue: 1.1220 time to fit residues: 290.3546 Evaluate side-chains 225 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 202 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 192 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 100 optimal weight: 0.0020 chunk 109 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN B 75 GLN B 119 ASN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS S 39 GLN S 167 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.205 Angle : 0.538 8.514 12178 Z= 0.273 Chirality : 0.041 0.199 1389 Planarity : 0.004 0.052 1526 Dihedral : 5.994 134.319 1231 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.76 % Allowed : 30.44 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1117 helix: 1.44 (0.25), residues: 407 sheet: -0.86 (0.30), residues: 282 loop : -1.00 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 62 PHE 0.010 0.001 PHE B 151 TYR 0.011 0.001 TYR R 190 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 216 GLU cc_start: 0.7508 (tt0) cc_final: 0.7296 (tt0) REVERT: A 231 ASP cc_start: 0.8473 (m-30) cc_final: 0.8101 (m-30) REVERT: A 243 MET cc_start: 0.7757 (tpp) cc_final: 0.7515 (tpt) REVERT: A 337 ASP cc_start: 0.8126 (m-30) cc_final: 0.7921 (m-30) REVERT: B 10 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6452 (tm-30) REVERT: B 14 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 67 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8159 (p) REVERT: B 120 ILE cc_start: 0.7999 (mm) cc_final: 0.7650 (mp) REVERT: B 197 ARG cc_start: 0.7866 (tpt170) cc_final: 0.7480 (mmp-170) REVERT: B 212 ASP cc_start: 0.7737 (t0) cc_final: 0.7245 (t0) REVERT: B 217 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7441 (pmt) REVERT: B 270 ILE cc_start: 0.8816 (pt) cc_final: 0.8579 (pp) REVERT: C 13 ARG cc_start: 0.7081 (ptp90) cc_final: 0.6826 (ptt-90) REVERT: C 29 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7994 (mtmm) REVERT: R 147 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6977 (tmm-80) REVERT: S 4 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (mt) REVERT: S 129 THR cc_start: 0.7898 (t) cc_final: 0.7587 (m) REVERT: S 159 ASN cc_start: 0.8020 (m-40) cc_final: 0.7630 (m-40) REVERT: S 180 MET cc_start: 0.4754 (tpp) cc_final: 0.4477 (tpp) REVERT: S 200 PHE cc_start: 0.8457 (m-80) cc_final: 0.8149 (m-80) REVERT: S 221 LEU cc_start: 0.8305 (tp) cc_final: 0.7970 (tm) REVERT: S 226 THR cc_start: 0.8398 (m) cc_final: 0.8126 (t) outliers start: 45 outliers final: 21 residues processed: 243 average time/residue: 1.0421 time to fit residues: 271.8442 Evaluate side-chains 225 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.4980 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.227 Angle : 0.538 8.471 12178 Z= 0.273 Chirality : 0.041 0.139 1389 Planarity : 0.004 0.050 1526 Dihedral : 6.008 135.527 1231 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.60 % Allowed : 30.97 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1117 helix: 1.48 (0.25), residues: 407 sheet: -0.85 (0.30), residues: 282 loop : -0.97 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.013 0.001 PHE R 94 TYR 0.011 0.001 TYR S 178 ARG 0.006 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7487 (tt) REVERT: A 53 MET cc_start: 0.8339 (mtm) cc_final: 0.8053 (mtt) REVERT: A 216 GLU cc_start: 0.7522 (tt0) cc_final: 0.7318 (tt0) REVERT: A 225 VAL cc_start: 0.8607 (t) cc_final: 0.8248 (m) REVERT: A 231 ASP cc_start: 0.8506 (m-30) cc_final: 0.8176 (m-30) REVERT: A 337 ASP cc_start: 0.8088 (m-30) cc_final: 0.7775 (m-30) REVERT: B 14 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7301 (mp) REVERT: B 67 SER cc_start: 0.8485 (OUTLIER) cc_final: 0.8168 (p) REVERT: B 120 ILE cc_start: 0.8039 (mm) cc_final: 0.7681 (mp) REVERT: B 146 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7976 (mt) REVERT: B 197 ARG cc_start: 0.7869 (tpt170) cc_final: 0.7478 (mmp-170) REVERT: B 212 ASP cc_start: 0.7733 (t0) cc_final: 0.7253 (t0) REVERT: B 217 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7457 (pmt) REVERT: B 270 ILE cc_start: 0.8820 (pt) cc_final: 0.8581 (pp) REVERT: C 29 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.8006 (mtmm) REVERT: R 147 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6984 (tmm-80) REVERT: S 4 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8064 (mt) REVERT: S 39 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8015 (tt0) REVERT: S 129 THR cc_start: 0.7901 (t) cc_final: 0.7596 (m) REVERT: S 159 ASN cc_start: 0.8016 (m-40) cc_final: 0.7644 (m-40) REVERT: S 180 MET cc_start: 0.4819 (tpp) cc_final: 0.4603 (tpp) REVERT: S 200 PHE cc_start: 0.8469 (m-80) cc_final: 0.8202 (m-80) REVERT: S 204 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7603 (mt) REVERT: S 221 LEU cc_start: 0.8317 (tp) cc_final: 0.7852 (tm) REVERT: S 222 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6690 (pm20) outliers start: 53 outliers final: 27 residues processed: 248 average time/residue: 1.1431 time to fit residues: 303.2910 Evaluate side-chains 247 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 209 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8988 Z= 0.298 Angle : 0.565 8.420 12178 Z= 0.288 Chirality : 0.042 0.275 1389 Planarity : 0.004 0.050 1526 Dihedral : 6.082 135.368 1231 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.55 % Allowed : 30.23 % Favored : 63.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.25), residues: 1117 helix: 1.47 (0.26), residues: 405 sheet: -0.93 (0.29), residues: 282 loop : -1.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.004 0.001 HIS B 91 PHE 0.016 0.002 PHE R 94 TYR 0.015 0.001 TYR S 178 ARG 0.005 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 218 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7478 (tt) REVERT: A 53 MET cc_start: 0.8334 (mtm) cc_final: 0.8025 (mtt) REVERT: A 192 LYS cc_start: 0.7943 (mptm) cc_final: 0.7703 (mptm) REVERT: A 225 VAL cc_start: 0.8601 (t) cc_final: 0.8228 (m) REVERT: A 337 ASP cc_start: 0.8085 (m-30) cc_final: 0.7757 (m-30) REVERT: B 10 GLU cc_start: 0.6652 (tm-30) cc_final: 0.6426 (tm-30) REVERT: B 14 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7366 (mp) REVERT: B 120 ILE cc_start: 0.8119 (mm) cc_final: 0.7823 (mp) REVERT: B 146 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8011 (mt) REVERT: B 197 ARG cc_start: 0.7873 (tpt170) cc_final: 0.7507 (mmp-170) REVERT: B 212 ASP cc_start: 0.7695 (t0) cc_final: 0.7216 (t0) REVERT: B 217 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7438 (pmt) REVERT: B 270 ILE cc_start: 0.8827 (pt) cc_final: 0.8581 (pp) REVERT: C 28 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8532 (pt) REVERT: C 29 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7992 (mtmm) REVERT: R 82 LEU cc_start: 0.7918 (mt) cc_final: 0.7620 (mp) REVERT: R 147 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6975 (tmm-80) REVERT: S 39 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: S 159 ASN cc_start: 0.8092 (m-40) cc_final: 0.7718 (m-40) REVERT: S 180 MET cc_start: 0.5262 (tpp) cc_final: 0.5035 (tpp) REVERT: S 200 PHE cc_start: 0.8465 (m-80) cc_final: 0.8208 (m-80) REVERT: S 204 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7653 (mt) REVERT: S 221 LEU cc_start: 0.8322 (tp) cc_final: 0.7868 (tm) REVERT: S 222 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6694 (pm20) outliers start: 62 outliers final: 28 residues processed: 256 average time/residue: 1.1110 time to fit residues: 304.2831 Evaluate side-chains 248 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 147 ARG Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 154 LEU Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.0370 chunk 56 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.193 Angle : 0.544 9.228 12178 Z= 0.273 Chirality : 0.042 0.274 1389 Planarity : 0.004 0.048 1526 Dihedral : 5.994 134.179 1231 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.39 % Allowed : 31.71 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1117 helix: 1.53 (0.26), residues: 405 sheet: -0.96 (0.29), residues: 286 loop : -1.00 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.020 0.001 PHE A 191 TYR 0.011 0.001 TYR R 190 ARG 0.005 0.000 ARG C 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 217 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7497 (tt) REVERT: A 53 MET cc_start: 0.8333 (mtm) cc_final: 0.8009 (mtt) REVERT: A 197 LYS cc_start: 0.8063 (mtmm) cc_final: 0.7356 (tptp) REVERT: A 337 ASP cc_start: 0.8082 (m-30) cc_final: 0.7776 (m-30) REVERT: B 10 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6446 (tm-30) REVERT: B 14 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7328 (mp) REVERT: B 67 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8187 (p) REVERT: B 120 ILE cc_start: 0.8027 (mm) cc_final: 0.7695 (mp) REVERT: B 146 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 197 ARG cc_start: 0.7876 (tpt170) cc_final: 0.7506 (mmp-170) REVERT: B 212 ASP cc_start: 0.7719 (t0) cc_final: 0.7329 (t0) REVERT: B 217 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7426 (pmt) REVERT: B 270 ILE cc_start: 0.8817 (pt) cc_final: 0.8574 (pp) REVERT: C 28 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8545 (pt) REVERT: C 29 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7950 (mtmm) REVERT: R 82 LEU cc_start: 0.8176 (mt) cc_final: 0.7855 (mp) REVERT: R 116 THR cc_start: 0.7768 (t) cc_final: 0.7567 (t) REVERT: S 60 TYR cc_start: 0.8303 (m-80) cc_final: 0.7904 (m-80) REVERT: S 159 ASN cc_start: 0.8070 (m-40) cc_final: 0.7736 (m-40) REVERT: S 221 LEU cc_start: 0.8308 (tp) cc_final: 0.7813 (tm) REVERT: S 222 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6642 (pm20) outliers start: 51 outliers final: 27 residues processed: 247 average time/residue: 1.1560 time to fit residues: 304.9756 Evaluate side-chains 243 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU 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: 5.9990 chunk 90 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 0.0980 chunk 42 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** 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: 0.7417 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.176 Angle : 0.540 9.353 12178 Z= 0.272 Chirality : 0.041 0.245 1389 Planarity : 0.004 0.047 1526 Dihedral : 5.934 132.676 1231 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.50 % Allowed : 32.24 % Favored : 62.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1117 helix: 1.58 (0.26), residues: 402 sheet: -0.94 (0.29), residues: 286 loop : -0.98 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE A 191 TYR 0.010 0.001 TYR R 190 ARG 0.012 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 212 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 49 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 53 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7975 (mtt) REVERT: A 197 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7310 (tptp) REVERT: A 231 ASP cc_start: 0.8472 (m-30) cc_final: 0.8138 (m-30) REVERT: A 243 MET cc_start: 0.7745 (tpp) cc_final: 0.7537 (tpt) REVERT: A 337 ASP cc_start: 0.8051 (m-30) cc_final: 0.7741 (m-30) REVERT: B 14 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7183 (mp) REVERT: B 20 ASP cc_start: 0.7303 (t70) cc_final: 0.7067 (t0) REVERT: B 120 ILE cc_start: 0.7986 (mm) cc_final: 0.7663 (mp) REVERT: B 146 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7971 (mt) REVERT: B 161 SER cc_start: 0.7973 (t) cc_final: 0.7611 (p) REVERT: B 197 ARG cc_start: 0.7862 (tpt170) cc_final: 0.7497 (mmp-170) REVERT: B 212 ASP cc_start: 0.7800 (t0) cc_final: 0.7406 (OUTLIER) REVERT: B 217 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7415 (pmt) REVERT: B 270 ILE cc_start: 0.8815 (pt) cc_final: 0.8572 (pp) REVERT: C 28 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8518 (pt) REVERT: C 29 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7932 (mtmm) REVERT: R 116 THR cc_start: 0.7787 (t) cc_final: 0.7571 (t) REVERT: S 60 TYR cc_start: 0.8295 (m-80) cc_final: 0.7937 (m-80) REVERT: S 221 LEU cc_start: 0.8282 (tp) cc_final: 0.7803 (tm) REVERT: S 222 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6680 (pm20) outliers start: 52 outliers final: 31 residues processed: 240 average time/residue: 1.1093 time to fit residues: 284.8206 Evaluate side-chains 242 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU 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: 1.9990 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8988 Z= 0.244 Angle : 0.580 13.249 12178 Z= 0.289 Chirality : 0.042 0.297 1389 Planarity : 0.004 0.048 1526 Dihedral : 6.037 133.369 1231 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 5.50 % Allowed : 32.56 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1117 helix: 1.49 (0.26), residues: 401 sheet: -0.98 (0.29), residues: 292 loop : -1.03 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE A 191 TYR 0.012 0.001 TYR S 178 ARG 0.015 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 217 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7964 (mtm) REVERT: A 243 MET cc_start: 0.7758 (tpp) cc_final: 0.7544 (tpt) REVERT: A 337 ASP cc_start: 0.8052 (m-30) cc_final: 0.7617 (m-30) REVERT: B 20 ASP cc_start: 0.7323 (t70) cc_final: 0.7057 (t0) REVERT: B 120 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7764 (mp) REVERT: B 146 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7930 (mt) REVERT: B 197 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7481 (mmp-170) REVERT: B 212 ASP cc_start: 0.7689 (t0) cc_final: 0.7296 (t0) REVERT: B 217 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7435 (pmt) REVERT: B 270 ILE cc_start: 0.8826 (pt) cc_final: 0.8579 (pp) REVERT: C 13 ARG cc_start: 0.7123 (ptp90) cc_final: 0.6700 (ptp90) REVERT: C 28 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8475 (pt) REVERT: C 29 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7993 (mtmm) REVERT: R 222 SER cc_start: 0.8288 (p) cc_final: 0.7879 (p) REVERT: R 224 SER cc_start: 0.8343 (m) cc_final: 0.7933 (p) REVERT: S 60 TYR cc_start: 0.8298 (m-80) cc_final: 0.7982 (m-80) REVERT: S 159 ASN cc_start: 0.7799 (m-40) cc_final: 0.7445 (m-40) REVERT: S 221 LEU cc_start: 0.8288 (tp) cc_final: 0.7812 (tm) REVERT: S 222 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6669 (pm20) outliers start: 52 outliers final: 30 residues processed: 245 average time/residue: 1.1578 time to fit residues: 303.7715 Evaluate side-chains 252 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 215 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 170 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 ILE Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 306 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 206 ARG Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.0050 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8988 Z= 0.202 Angle : 0.580 12.182 12178 Z= 0.286 Chirality : 0.041 0.276 1389 Planarity : 0.004 0.047 1526 Dihedral : 6.005 133.070 1231 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.23 % Allowed : 34.14 % Favored : 61.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1117 helix: 1.56 (0.26), residues: 401 sheet: -0.92 (0.29), residues: 288 loop : -1.00 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.012 0.001 PHE A 191 TYR 0.011 0.001 TYR S 101 ARG 0.013 0.000 ARG C 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 215 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8013 (mtm) REVERT: A 243 MET cc_start: 0.7749 (tpp) cc_final: 0.7532 (tpt) REVERT: A 337 ASP cc_start: 0.8052 (m-30) cc_final: 0.7627 (m-30) REVERT: B 20 ASP cc_start: 0.7308 (t70) cc_final: 0.7074 (t0) REVERT: B 52 ARG cc_start: 0.7335 (mtm180) cc_final: 0.7044 (ttm110) REVERT: B 120 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7712 (mp) REVERT: B 146 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7988 (mt) REVERT: B 161 SER cc_start: 0.8040 (t) cc_final: 0.7682 (p) REVERT: B 197 ARG cc_start: 0.7858 (tpt170) cc_final: 0.7490 (mmp-170) REVERT: B 212 ASP cc_start: 0.7808 (t0) cc_final: 0.7412 (t0) REVERT: B 217 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7441 (pmt) REVERT: B 270 ILE cc_start: 0.8821 (pt) cc_final: 0.8574 (pp) REVERT: C 28 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8474 (pt) REVERT: C 29 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7959 (mtmm) REVERT: R 222 SER cc_start: 0.8276 (p) cc_final: 0.7871 (p) REVERT: R 224 SER cc_start: 0.8273 (m) cc_final: 0.7897 (p) REVERT: S 60 TYR cc_start: 0.8286 (m-80) cc_final: 0.7983 (m-80) REVERT: S 159 ASN cc_start: 0.7894 (m-40) cc_final: 0.7557 (m-40) REVERT: S 164 TRP cc_start: 0.8604 (m100) cc_final: 0.8391 (m100) REVERT: S 221 LEU cc_start: 0.8296 (tp) cc_final: 0.7804 (tm) REVERT: S 222 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6678 (pm20) outliers start: 40 outliers final: 26 residues processed: 237 average time/residue: 1.0684 time to fit residues: 272.3207 Evaluate side-chains 247 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU 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: 0.4980 chunk 110 optimal weight: 0.2980 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.0470 chunk 9 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 95 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8988 Z= 0.180 Angle : 0.579 12.056 12178 Z= 0.286 Chirality : 0.041 0.264 1389 Planarity : 0.004 0.047 1526 Dihedral : 5.989 133.973 1231 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.49 % Allowed : 34.99 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1117 helix: 1.61 (0.26), residues: 403 sheet: -0.97 (0.30), residues: 284 loop : -1.00 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.014 0.001 PHE A 191 TYR 0.009 0.001 TYR R 190 ARG 0.012 0.000 ARG C 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2234 Ramachandran restraints generated. 1117 Oldfield, 0 Emsley, 1117 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 53 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8001 (mtt) REVERT: A 197 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7322 (tptp) REVERT: A 243 MET cc_start: 0.7741 (tpp) cc_final: 0.7529 (tpt) REVERT: A 337 ASP cc_start: 0.8045 (m-30) cc_final: 0.7595 (m-30) REVERT: B 20 ASP cc_start: 0.7267 (t70) cc_final: 0.7013 (t0) REVERT: B 120 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7653 (mp) REVERT: B 146 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7990 (mt) REVERT: B 161 SER cc_start: 0.8011 (t) cc_final: 0.7675 (p) REVERT: B 197 ARG cc_start: 0.7858 (tpt170) cc_final: 0.7484 (mmp-170) REVERT: B 212 ASP cc_start: 0.7827 (t0) cc_final: 0.7368 (OUTLIER) REVERT: B 217 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7459 (pmt) REVERT: B 270 ILE cc_start: 0.8816 (pt) cc_final: 0.8569 (pp) REVERT: B 314 ARG cc_start: 0.8369 (ttm170) cc_final: 0.8111 (ptp-170) REVERT: C 29 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7930 (mtmm) REVERT: R 222 SER cc_start: 0.8267 (p) cc_final: 0.7842 (p) REVERT: R 224 SER cc_start: 0.8202 (m) cc_final: 0.7850 (p) REVERT: S 159 ASN cc_start: 0.7908 (m-40) cc_final: 0.7584 (m-40) REVERT: S 164 TRP cc_start: 0.8711 (m100) cc_final: 0.8222 (m100) REVERT: S 221 LEU cc_start: 0.8281 (tp) cc_final: 0.7811 (tm) REVERT: S 222 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6693 (pm20) outliers start: 33 outliers final: 24 residues processed: 237 average time/residue: 1.1066 time to fit residues: 281.2941 Evaluate side-chains 240 residues out of total 966 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain R residue 33 LYS Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 67 LYS Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 222 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 220 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.124036 restraints weight = 13320.057| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.25 r_work: 0.3540 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8988 Z= 0.219 Angle : 0.596 12.927 12178 Z= 0.296 Chirality : 0.042 0.269 1389 Planarity : 0.004 0.047 1526 Dihedral : 6.046 134.026 1231 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.33 % Allowed : 34.14 % Favored : 61.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1117 helix: 1.58 (0.26), residues: 403 sheet: -0.90 (0.29), residues: 285 loop : -1.04 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.024 0.001 PHE A 191 TYR 0.013 0.001 TYR S 60 ARG 0.015 0.000 ARG C 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4490.17 seconds wall clock time: 80 minutes 12.35 seconds (4812.35 seconds total)