Starting phenix.real_space_refine on Wed Feb 14 09:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kfx_37207/02_2024/8kfx_37207_updated.pdb" } resolution = 2.96 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 5762 2.51 5 N 1506 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 8": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9001 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: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'OS9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.89, per 1000 atoms: 0.54 Number of scatterers: 9001 At special positions: 0 Unit cell: (89.44, 121.68, 130, 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 1506 7.00 C 5762 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=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 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: 3.62 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: 29 helices and 15 sheets defined 35.6% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 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 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 230 removed outlier: 3.872A 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 271 through 279 removed outlier: 4.427A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (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 310 removed outlier: 3.730A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 24 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 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'R' and resid 31 through 61 Processing helix chain 'R' and resid 69 through 96 removed outlier: 4.147A pdb=" N SER R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) removed outlier: 4.471A 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: 3.749A 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 removed outlier: 3.777A pdb=" N VAL R 170 " --> pdb=" O ILE R 166 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N PHE R 171 " --> pdb=" O PRO R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 204 removed outlier: 3.579A pdb=" N MET R 202 " --> pdb=" O THR R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 226 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: 4.646A pdb=" N HIS R 292 " --> pdb=" O ILE R 288 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N CYS R 293 " --> pdb=" O SER R 289 " (cutoff:3.500A) removed outlier: 4.294A 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 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' 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: 6.655A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.816A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.079A 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: 6.927A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.820A 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: 6.742A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.893A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.625A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.852A 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: 6.526A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.455A 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: 6.704A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.210A 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 10 through 12 Processing sheet with id= K, first strand: chain 'S' and resid 17 through 23 Processing sheet with id= L, first strand: chain 'S' and resid 95 through 99 removed outlier: 3.509A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.332A 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: 5.891A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 416 hydrogen bonds defined for protein. 1191 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: 2.73 Time building geometry restraints manager: 3.90 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: 2861 1.34 - 1.46: 2235 1.46 - 1.58: 4001 1.58 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9193 Sorted by residual: bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.473 1.624 -0.151 1.40e-02 5.10e+03 1.17e+02 bond pdb=" C21 OS9 R 601 " pdb=" N3 OS9 R 601 " ideal model delta sigma weight residual 1.383 1.472 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C21 OS9 R 601 " pdb=" N2 OS9 R 601 " ideal model delta sigma weight residual 1.564 1.479 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C17 OS9 R 601 " pdb=" N3 OS9 R 601 " ideal model delta sigma weight residual 1.537 1.465 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" C12 OS9 R 601 " pdb=" C14 OS9 R 601 " ideal model delta sigma weight residual 1.571 1.510 0.061 2.00e-02 2.50e+03 9.22e+00 ... (remaining 9188 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 122 105.89 - 112.94: 4988 112.94 - 119.98: 3075 119.98 - 127.02: 4169 127.02 - 134.07: 90 Bond angle restraints: 12444 Sorted by residual: angle pdb=" C2 OS9 R 601 " pdb=" C7 OS9 R 601 " pdb=" O2 OS9 R 601 " ideal model delta sigma weight residual 103.53 118.11 -14.58 3.00e+00 1.11e-01 2.36e+01 angle pdb=" N THR R 291 " pdb=" CA THR R 291 " pdb=" C THR R 291 " ideal model delta sigma weight residual 112.34 107.46 4.88 1.30e+00 5.92e-01 1.41e+01 angle pdb=" C6 OS9 R 601 " pdb=" C7 OS9 R 601 " pdb=" O2 OS9 R 601 " ideal model delta sigma weight residual 132.86 121.64 11.22 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN A 52 " pdb=" CB GLN A 52 " pdb=" CG GLN A 52 " ideal model delta sigma weight residual 114.10 121.50 -7.40 2.00e+00 2.50e-01 1.37e+01 angle pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta sigma weight residual 121.80 113.02 8.78 2.44e+00 1.68e-01 1.29e+01 ... (remaining 12439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4689 17.91 - 35.82: 558 35.82 - 53.73: 163 53.73 - 71.65: 22 71.65 - 89.56: 7 Dihedral angle restraints: 5439 sinusoidal: 2125 harmonic: 3314 Sorted by residual: dihedral pdb=" CA TYR S 223 " pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+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 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 5436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 821 0.028 - 0.057: 354 0.057 - 0.085: 154 0.085 - 0.114: 71 0.114 - 0.142: 14 Chirality restraints: 1414 Sorted by residual: chirality pdb=" CB ILE S 70 " pdb=" CA ILE S 70 " pdb=" CG1 ILE S 70 " pdb=" CG2 ILE S 70 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.05e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA PHE R 41 " pdb=" N PHE R 41 " pdb=" C PHE R 41 " pdb=" CB PHE R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1411 not shown) Planarity restraints: 1558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.040 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO S 224 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 186 " -0.011 2.00e-02 2.50e+03 1.64e-02 4.71e+00 pdb=" CG PHE R 186 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 186 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE R 186 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE R 186 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 186 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 186 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 170 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" CG ASP B 170 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 170 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 170 " -0.012 2.00e-02 2.50e+03 ... (remaining 1555 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 567 2.73 - 3.27: 8922 3.27 - 3.82: 15450 3.82 - 4.36: 18567 4.36 - 4.90: 31929 Nonbonded interactions: 75435 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.189 2.440 nonbonded pdb=" O LEU R 50 " pdb=" OG SER R 54 " model vdw 2.204 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.208 2.440 nonbonded pdb=" ND1 HIS B 54 " pdb=" OG SER B 74 " model vdw 2.252 2.520 nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.267 2.520 ... (remaining 75430 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: 1.070 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: 3.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 0.151 9193 Z= 0.284 Angle : 0.666 14.583 12444 Z= 0.340 Chirality : 0.042 0.142 1414 Planarity : 0.004 0.058 1558 Dihedral : 16.752 89.558 3292 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.51 % Allowed : 30.16 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.90 (0.25), residues: 1125 helix: 2.18 (0.27), residues: 398 sheet: 0.30 (0.30), residues: 286 loop : -0.64 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.037 0.002 PHE R 186 TYR 0.016 0.001 TYR R 94 ARG 0.013 0.001 ARG S 148 *********************** 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 257 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 252 time to evaluate : 0.985 Fit side-chains REVERT: A 231 ASP cc_start: 0.7629 (t0) cc_final: 0.7403 (t0) REVERT: A 340 THR cc_start: 0.8656 (m) cc_final: 0.8351 (t) REVERT: B 19 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7279 (mtm110) REVERT: B 61 MET cc_start: 0.8231 (tmm) cc_final: 0.7993 (ppp) REVERT: R 117 PHE cc_start: 0.8151 (t80) cc_final: 0.7919 (t80) REVERT: R 121 MET cc_start: 0.8187 (tpp) cc_final: 0.7617 (mpp) REVERT: R 216 PHE cc_start: 0.8045 (t80) cc_final: 0.7738 (t80) outliers start: 5 outliers final: 4 residues processed: 256 average time/residue: 1.1211 time to fit residues: 306.8204 Evaluate side-chains 246 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 242 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain S residue 130 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9193 Z= 0.316 Angle : 0.549 10.087 12444 Z= 0.288 Chirality : 0.042 0.173 1414 Planarity : 0.004 0.061 1558 Dihedral : 6.434 83.402 1250 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.67 % Favored : 97.24 % Rotamer: Outliers : 3.74 % Allowed : 26.32 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % 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: 0.90 (0.25), residues: 1125 helix: 2.22 (0.26), residues: 400 sheet: 0.24 (0.30), residues: 293 loop : -0.69 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.027 0.002 PHE R 290 TYR 0.012 0.002 TYR R 113 ARG 0.005 0.001 ARG S 148 *********************** 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 283 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 246 time to evaluate : 0.931 Fit side-chains REVERT: A 186 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6385 (tm-30) REVERT: A 231 ASP cc_start: 0.7672 (t0) cc_final: 0.7398 (t0) REVERT: A 310 LEU cc_start: 0.8645 (mt) cc_final: 0.8400 (mp) REVERT: B 61 MET cc_start: 0.8239 (tmm) cc_final: 0.7967 (ppp) REVERT: B 197 ARG cc_start: 0.7255 (mpt-90) cc_final: 0.7010 (mtt-85) REVERT: B 219 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7684 (mtt-85) REVERT: B 234 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 258 ASP cc_start: 0.7734 (t0) cc_final: 0.7445 (t0) REVERT: R 37 LEU cc_start: 0.7262 (tp) cc_final: 0.6836 (tm) REVERT: R 41 PHE cc_start: 0.7690 (m-80) cc_final: 0.7213 (m-80) REVERT: R 46 PHE cc_start: 0.7748 (t80) cc_final: 0.7449 (t80) REVERT: R 51 LEU cc_start: 0.8306 (mt) cc_final: 0.8094 (mt) REVERT: R 55 LEU cc_start: 0.8365 (tm) cc_final: 0.8049 (tt) REVERT: R 95 LEU cc_start: 0.8436 (mt) cc_final: 0.8207 (mm) REVERT: R 105 MET cc_start: 0.7210 (mmm) cc_final: 0.6856 (tmm) REVERT: R 235 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7497 (mmmm) REVERT: S 39 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: S 87 ARG cc_start: 0.7490 (pmm-80) cc_final: 0.7047 (ptt90) REVERT: S 110 PHE cc_start: 0.8618 (t80) cc_final: 0.8327 (t80) REVERT: S 223 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7746 (t80) outliers start: 37 outliers final: 20 residues processed: 267 average time/residue: 1.1153 time to fit residues: 318.3614 Evaluate side-chains 262 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 238 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9193 Z= 0.218 Angle : 0.501 8.271 12444 Z= 0.262 Chirality : 0.040 0.142 1414 Planarity : 0.003 0.063 1558 Dihedral : 6.211 79.012 1247 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.05 % Allowed : 26.21 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1125 helix: 2.41 (0.26), residues: 400 sheet: 0.23 (0.30), residues: 289 loop : -0.64 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.027 0.002 PHE R 117 TYR 0.013 0.001 TYR R 172 ARG 0.004 0.000 ARG S 148 *********************** 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 286 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 0.866 Fit side-chains REVERT: A 193 ASP cc_start: 0.7754 (t0) cc_final: 0.7309 (t0) REVERT: A 231 ASP cc_start: 0.7694 (t0) cc_final: 0.7405 (t0) REVERT: B 19 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7127 (ttp80) REVERT: B 22 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6839 (mtt180) REVERT: B 61 MET cc_start: 0.8232 (tmm) cc_final: 0.7976 (ppp) REVERT: B 197 ARG cc_start: 0.7263 (mpt-90) cc_final: 0.6954 (mtt-85) REVERT: B 219 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7706 (mtt90) REVERT: B 258 ASP cc_start: 0.7777 (t0) cc_final: 0.7233 (t0) REVERT: R 37 LEU cc_start: 0.7224 (tp) cc_final: 0.6848 (tm) REVERT: R 41 PHE cc_start: 0.7753 (m-80) cc_final: 0.7291 (m-80) REVERT: R 46 PHE cc_start: 0.7717 (t80) cc_final: 0.7389 (t80) REVERT: R 51 LEU cc_start: 0.8333 (mt) cc_final: 0.8097 (mt) REVERT: R 55 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8043 (tt) REVERT: R 95 LEU cc_start: 0.8443 (mt) cc_final: 0.8199 (mm) REVERT: R 105 MET cc_start: 0.7212 (mmm) cc_final: 0.6809 (tmm) REVERT: R 219 ILE cc_start: 0.8780 (mm) cc_final: 0.8556 (mt) REVERT: S 87 ARG cc_start: 0.7485 (pmm-80) cc_final: 0.7077 (ptt90) REVERT: S 110 PHE cc_start: 0.8564 (t80) cc_final: 0.8325 (t80) REVERT: S 172 SER cc_start: 0.8219 (p) cc_final: 0.7990 (t) REVERT: S 200 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: S 223 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7784 (t80) outliers start: 40 outliers final: 23 residues processed: 264 average time/residue: 1.1214 time to fit residues: 316.5604 Evaluate side-chains 273 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 247 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 171 GLN Chi-restraints excluded: chain S residue 200 PHE 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: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 60 optimal weight: 7.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 ASN ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9193 Z= 0.248 Angle : 0.504 7.536 12444 Z= 0.265 Chirality : 0.040 0.143 1414 Planarity : 0.004 0.064 1558 Dihedral : 6.205 77.577 1247 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.67 % Allowed : 25.10 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1125 helix: 2.44 (0.26), residues: 400 sheet: 0.19 (0.29), residues: 296 loop : -0.65 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.027 0.002 PHE R 117 TYR 0.011 0.001 TYR S 178 ARG 0.004 0.000 ARG S 148 *********************** 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 304 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 248 time to evaluate : 1.045 Fit side-chains REVERT: A 24 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6909 (mtm-85) REVERT: A 193 ASP cc_start: 0.7757 (t0) cc_final: 0.7312 (t0) REVERT: A 197 LYS cc_start: 0.8496 (mtmm) cc_final: 0.8270 (mtpp) REVERT: A 231 ASP cc_start: 0.7711 (t0) cc_final: 0.7417 (t0) REVERT: B 19 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7172 (ttp80) REVERT: B 22 ARG cc_start: 0.7145 (mtt180) cc_final: 0.6771 (mtt180) REVERT: B 61 MET cc_start: 0.8242 (tmm) cc_final: 0.7982 (ppp) REVERT: B 197 ARG cc_start: 0.7265 (mpt-90) cc_final: 0.6954 (mtt-85) REVERT: B 214 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7050 (mmt180) REVERT: B 219 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7716 (mtt90) REVERT: B 234 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8392 (m-80) REVERT: B 258 ASP cc_start: 0.7689 (t0) cc_final: 0.7076 (t0) REVERT: R 37 LEU cc_start: 0.7211 (tp) cc_final: 0.6879 (tm) REVERT: R 41 PHE cc_start: 0.7789 (m-80) cc_final: 0.7434 (m-80) REVERT: R 46 PHE cc_start: 0.7652 (t80) cc_final: 0.7325 (t80) REVERT: R 55 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8038 (tt) REVERT: R 95 LEU cc_start: 0.8447 (mt) cc_final: 0.8208 (mm) REVERT: R 105 MET cc_start: 0.7233 (mmm) cc_final: 0.6825 (mmm) REVERT: R 204 ILE cc_start: 0.8548 (pp) cc_final: 0.8348 (pt) REVERT: R 235 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7473 (mmmm) REVERT: S 39 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7555 (tp40) REVERT: S 172 SER cc_start: 0.8246 (p) cc_final: 0.8015 (t) REVERT: S 223 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7821 (t80) outliers start: 56 outliers final: 32 residues processed: 277 average time/residue: 1.1101 time to fit residues: 328.8858 Evaluate side-chains 284 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN 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: 0.8980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9193 Z= 0.255 Angle : 0.510 7.532 12444 Z= 0.267 Chirality : 0.040 0.141 1414 Planarity : 0.003 0.064 1558 Dihedral : 6.164 75.369 1247 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.36 % Allowed : 25.91 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1125 helix: 2.48 (0.26), residues: 400 sheet: 0.22 (0.29), residues: 296 loop : -0.64 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.024 0.002 PHE R 117 TYR 0.012 0.001 TYR R 172 ARG 0.003 0.000 ARG S 148 *********************** 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 307 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 254 time to evaluate : 0.964 Fit side-chains REVERT: A 24 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.6910 (mtm-85) REVERT: A 193 ASP cc_start: 0.7752 (t0) cc_final: 0.7309 (t0) REVERT: A 231 ASP cc_start: 0.7714 (t0) cc_final: 0.7410 (t0) REVERT: A 328 ASP cc_start: 0.7782 (m-30) cc_final: 0.7447 (OUTLIER) REVERT: B 19 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7185 (ttp80) REVERT: B 22 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6793 (mtt180) REVERT: B 61 MET cc_start: 0.8230 (tmm) cc_final: 0.7985 (ppp) REVERT: B 128 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.8245 (t) REVERT: B 197 ARG cc_start: 0.7274 (mpt-90) cc_final: 0.6951 (mtt-85) REVERT: B 214 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7075 (mmt180) REVERT: B 219 ARG cc_start: 0.7940 (mtp85) cc_final: 0.7701 (mtt-85) REVERT: B 234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8411 (m-80) REVERT: B 258 ASP cc_start: 0.7770 (t0) cc_final: 0.7112 (t0) REVERT: R 37 LEU cc_start: 0.7192 (tp) cc_final: 0.6834 (tm) REVERT: R 41 PHE cc_start: 0.7824 (m-80) cc_final: 0.7485 (m-80) REVERT: R 46 PHE cc_start: 0.7637 (t80) cc_final: 0.7334 (t80) REVERT: R 55 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8039 (tt) REVERT: R 95 LEU cc_start: 0.8478 (mt) cc_final: 0.8205 (mm) REVERT: R 105 MET cc_start: 0.7230 (mmm) cc_final: 0.6891 (mmm) REVERT: R 235 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7468 (mmmm) REVERT: S 39 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: S 87 ARG cc_start: 0.7459 (pmm-80) cc_final: 0.7095 (ptt90) REVERT: S 150 SER cc_start: 0.8767 (t) cc_final: 0.8472 (p) REVERT: S 172 SER cc_start: 0.8236 (p) cc_final: 0.8002 (t) REVERT: S 223 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7833 (t80) outliers start: 53 outliers final: 30 residues processed: 277 average time/residue: 1.1036 time to fit residues: 327.1500 Evaluate side-chains 285 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 249 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR 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: 1.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9193 Z= 0.281 Angle : 0.530 11.409 12444 Z= 0.275 Chirality : 0.041 0.143 1414 Planarity : 0.004 0.065 1558 Dihedral : 6.089 73.763 1245 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.96 % Allowed : 26.62 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.25), residues: 1125 helix: 2.42 (0.26), residues: 400 sheet: 0.23 (0.29), residues: 296 loop : -0.67 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.002 PHE S 68 TYR 0.013 0.001 TYR R 172 ARG 0.004 0.000 ARG S 18 *********************** 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 301 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.006 Fit side-chains REVERT: A 24 ARG cc_start: 0.7267 (mtm-85) cc_final: 0.6913 (mtm-85) REVERT: A 193 ASP cc_start: 0.7752 (t0) cc_final: 0.7307 (t0) REVERT: A 231 ASP cc_start: 0.7686 (t0) cc_final: 0.7390 (t0) REVERT: A 328 ASP cc_start: 0.7786 (m-30) cc_final: 0.7471 (OUTLIER) REVERT: B 19 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7219 (ttp80) REVERT: B 22 ARG cc_start: 0.7163 (mtt180) cc_final: 0.6829 (mtt180) REVERT: B 61 MET cc_start: 0.8243 (tmm) cc_final: 0.7985 (ppp) REVERT: B 128 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8242 (t) REVERT: B 197 ARG cc_start: 0.7294 (mpt-90) cc_final: 0.6964 (mtt-85) REVERT: B 214 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7070 (mmt180) REVERT: B 219 ARG cc_start: 0.7944 (mtp85) cc_final: 0.7701 (mtt-85) REVERT: B 234 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: B 258 ASP cc_start: 0.7815 (t0) cc_final: 0.7168 (t0) REVERT: R 37 LEU cc_start: 0.7199 (tp) cc_final: 0.6838 (tm) REVERT: R 41 PHE cc_start: 0.7844 (m-80) cc_final: 0.7512 (m-80) REVERT: R 46 PHE cc_start: 0.7615 (t80) cc_final: 0.7328 (t80) REVERT: R 55 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8047 (tt) REVERT: R 95 LEU cc_start: 0.8439 (mt) cc_final: 0.8157 (mm) REVERT: R 105 MET cc_start: 0.7249 (mmm) cc_final: 0.6911 (mmm) REVERT: R 235 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7472 (mmmm) REVERT: S 39 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: S 150 SER cc_start: 0.8786 (t) cc_final: 0.8480 (p) REVERT: S 172 SER cc_start: 0.8232 (p) cc_final: 0.7994 (t) REVERT: S 223 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7786 (t80) outliers start: 49 outliers final: 33 residues processed: 273 average time/residue: 1.1456 time to fit residues: 334.4643 Evaluate side-chains 287 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 248 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 225 LEU 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: 6.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 chunk 32 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9193 Z= 0.202 Angle : 0.504 10.815 12444 Z= 0.261 Chirality : 0.039 0.137 1414 Planarity : 0.003 0.063 1558 Dihedral : 5.973 72.091 1245 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.76 % Allowed : 26.82 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1125 helix: 2.49 (0.26), residues: 400 sheet: 0.24 (0.30), residues: 291 loop : -0.63 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS S 35 PHE 0.029 0.002 PHE R 117 TYR 0.011 0.001 TYR R 114 ARG 0.006 0.000 ARG S 148 *********************** 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 298 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 251 time to evaluate : 1.038 Fit side-chains REVERT: A 24 ARG cc_start: 0.7258 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: A 193 ASP cc_start: 0.7734 (t0) cc_final: 0.7294 (t0) REVERT: A 231 ASP cc_start: 0.7590 (t0) cc_final: 0.7286 (t0) REVERT: A 310 LEU cc_start: 0.8569 (mt) cc_final: 0.8355 (mp) REVERT: A 328 ASP cc_start: 0.7811 (m-30) cc_final: 0.7500 (OUTLIER) REVERT: B 19 ARG cc_start: 0.7575 (ttp80) cc_final: 0.7202 (ttp80) REVERT: B 22 ARG cc_start: 0.7210 (mtt180) cc_final: 0.6795 (mtt180) REVERT: B 61 MET cc_start: 0.8248 (tmm) cc_final: 0.7984 (ppp) REVERT: B 128 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8254 (t) REVERT: B 197 ARG cc_start: 0.7282 (mpt-90) cc_final: 0.6941 (mtt-85) REVERT: B 214 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.7067 (mmt180) REVERT: B 258 ASP cc_start: 0.7808 (t0) cc_final: 0.7144 (t0) REVERT: B 283 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8272 (tpt170) REVERT: R 37 LEU cc_start: 0.7167 (tp) cc_final: 0.6801 (tm) REVERT: R 41 PHE cc_start: 0.7841 (m-80) cc_final: 0.7504 (m-80) REVERT: R 46 PHE cc_start: 0.7561 (t80) cc_final: 0.7246 (t80) REVERT: R 55 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8010 (tt) REVERT: R 95 LEU cc_start: 0.8422 (mt) cc_final: 0.8163 (mm) REVERT: R 105 MET cc_start: 0.7181 (mmm) cc_final: 0.6865 (mmm) REVERT: R 235 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7455 (mmmm) REVERT: S 150 SER cc_start: 0.8772 (t) cc_final: 0.8461 (p) REVERT: S 172 SER cc_start: 0.8243 (p) cc_final: 0.8015 (t) REVERT: S 223 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7777 (t80) outliers start: 47 outliers final: 27 residues processed: 273 average time/residue: 1.0710 time to fit residues: 313.2019 Evaluate side-chains 282 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 171 GLN 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: 0.5980 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9193 Z= 0.223 Angle : 0.526 11.819 12444 Z= 0.272 Chirality : 0.040 0.138 1414 Planarity : 0.003 0.063 1558 Dihedral : 5.956 70.785 1245 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.25 % Allowed : 27.83 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.25), residues: 1125 helix: 2.48 (0.26), residues: 400 sheet: 0.28 (0.30), residues: 289 loop : -0.65 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE R 117 TYR 0.010 0.001 TYR R 172 ARG 0.005 0.000 ARG S 148 *********************** 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 294 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 252 time to evaluate : 1.047 Fit side-chains REVERT: A 24 ARG cc_start: 0.7254 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: A 193 ASP cc_start: 0.7731 (t0) cc_final: 0.7295 (t0) REVERT: A 231 ASP cc_start: 0.7582 (t0) cc_final: 0.7290 (t0) REVERT: A 269 ASN cc_start: 0.8186 (m-40) cc_final: 0.7955 (m-40) REVERT: A 310 LEU cc_start: 0.8561 (mt) cc_final: 0.8353 (mp) REVERT: A 328 ASP cc_start: 0.7815 (m-30) cc_final: 0.7510 (OUTLIER) REVERT: A 340 THR cc_start: 0.8634 (m) cc_final: 0.8180 (m) REVERT: B 19 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7136 (ttp80) REVERT: B 22 ARG cc_start: 0.7185 (mtt180) cc_final: 0.6811 (mtt180) REVERT: B 61 MET cc_start: 0.8254 (tmm) cc_final: 0.7989 (ppp) REVERT: B 128 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8255 (t) REVERT: B 197 ARG cc_start: 0.7278 (mpt-90) cc_final: 0.6939 (mtt-85) REVERT: B 214 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7079 (mmt180) REVERT: B 219 ARG cc_start: 0.7926 (mtp85) cc_final: 0.7682 (mtt-85) REVERT: B 234 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8443 (m-80) REVERT: B 258 ASP cc_start: 0.7794 (t0) cc_final: 0.7085 (t0) REVERT: R 37 LEU cc_start: 0.7161 (tp) cc_final: 0.6790 (tm) REVERT: R 41 PHE cc_start: 0.7848 (m-80) cc_final: 0.7511 (m-80) REVERT: R 46 PHE cc_start: 0.7555 (t80) cc_final: 0.7234 (t80) REVERT: R 55 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8014 (tt) REVERT: R 95 LEU cc_start: 0.8428 (mt) cc_final: 0.8203 (mm) REVERT: R 105 MET cc_start: 0.7213 (mmm) cc_final: 0.6843 (mmm) REVERT: R 121 MET cc_start: 0.8282 (tpp) cc_final: 0.7563 (mpp) REVERT: R 235 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7454 (mmmm) REVERT: S 150 SER cc_start: 0.8776 (t) cc_final: 0.8470 (p) REVERT: S 172 SER cc_start: 0.8245 (p) cc_final: 0.8021 (t) REVERT: S 223 TYR cc_start: 0.8064 (OUTLIER) cc_final: 0.7790 (t80) outliers start: 42 outliers final: 29 residues processed: 270 average time/residue: 1.1430 time to fit residues: 330.4171 Evaluate side-chains 281 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 247 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 287 ILE Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 146 SER 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: 2.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 105 optimal weight: 0.0370 chunk 64 optimal weight: 0.3980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9193 Z= 0.170 Angle : 0.516 11.706 12444 Z= 0.266 Chirality : 0.040 0.136 1414 Planarity : 0.003 0.063 1558 Dihedral : 5.858 70.095 1245 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.25 % Allowed : 28.14 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1125 helix: 2.44 (0.26), residues: 402 sheet: 0.37 (0.30), residues: 288 loop : -0.63 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.023 0.002 PHE R 117 TYR 0.011 0.001 TYR S 178 ARG 0.004 0.000 ARG S 148 *********************** 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 304 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 262 time to evaluate : 1.075 Fit side-chains REVERT: A 24 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.6937 (mtm-85) REVERT: A 193 ASP cc_start: 0.7742 (t0) cc_final: 0.7301 (t0) REVERT: A 269 ASN cc_start: 0.8178 (m-40) cc_final: 0.7941 (m-40) REVERT: A 285 ILE cc_start: 0.8367 (tt) cc_final: 0.8107 (pp) REVERT: A 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8326 (mp) REVERT: A 328 ASP cc_start: 0.7810 (m-30) cc_final: 0.7508 (OUTLIER) REVERT: A 340 THR cc_start: 0.8659 (m) cc_final: 0.8226 (m) REVERT: B 19 ARG cc_start: 0.7509 (ttp80) cc_final: 0.7150 (ttp80) REVERT: B 22 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6883 (mtt180) REVERT: B 61 MET cc_start: 0.8270 (tmm) cc_final: 0.7900 (ppp) REVERT: B 128 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 197 ARG cc_start: 0.7264 (mpt-90) cc_final: 0.6929 (mtt-85) REVERT: B 214 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.7078 (mmt180) REVERT: B 219 ARG cc_start: 0.7987 (mtp85) cc_final: 0.7748 (mtt-85) REVERT: B 258 ASP cc_start: 0.7773 (t0) cc_final: 0.7178 (t0) REVERT: R 37 LEU cc_start: 0.7129 (tp) cc_final: 0.6763 (tm) REVERT: R 41 PHE cc_start: 0.7834 (m-80) cc_final: 0.7464 (m-80) REVERT: R 55 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7944 (tt) REVERT: R 105 MET cc_start: 0.7298 (mmm) cc_final: 0.6923 (mmm) REVERT: R 204 ILE cc_start: 0.8421 (pp) cc_final: 0.8185 (pt) REVERT: R 235 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7451 (mmmm) REVERT: S 39 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7510 (tp40) REVERT: S 98 ARG cc_start: 0.8719 (ptm160) cc_final: 0.8442 (ptm160) REVERT: S 150 SER cc_start: 0.8764 (t) cc_final: 0.8452 (p) REVERT: S 223 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7778 (t80) outliers start: 42 outliers final: 26 residues processed: 278 average time/residue: 1.1936 time to fit residues: 356.3828 Evaluate side-chains 286 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 255 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 128 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 110 optimal weight: 0.0170 chunk 101 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9193 Z= 0.198 Angle : 0.540 11.741 12444 Z= 0.274 Chirality : 0.041 0.296 1414 Planarity : 0.003 0.063 1558 Dihedral : 5.855 70.080 1245 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.54 % Allowed : 29.86 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1125 helix: 2.38 (0.26), residues: 403 sheet: 0.38 (0.30), residues: 288 loop : -0.64 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.001 PHE R 214 TYR 0.017 0.001 TYR R 300 ARG 0.004 0.000 ARG S 148 ********************** 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 288 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 0.988 Fit side-chains REVERT: A 24 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: A 193 ASP cc_start: 0.7744 (t0) cc_final: 0.7301 (t0) REVERT: A 231 ASP cc_start: 0.7858 (t0) cc_final: 0.7442 (m-30) REVERT: A 269 ASN cc_start: 0.8183 (m-40) cc_final: 0.7964 (m110) REVERT: A 285 ILE cc_start: 0.8359 (tt) cc_final: 0.8083 (pp) REVERT: A 310 LEU cc_start: 0.8552 (mt) cc_final: 0.8326 (mp) REVERT: A 328 ASP cc_start: 0.7815 (m-30) cc_final: 0.7510 (OUTLIER) REVERT: A 340 THR cc_start: 0.8663 (m) cc_final: 0.8240 (m) REVERT: B 19 ARG cc_start: 0.7514 (ttp80) cc_final: 0.7152 (ttp80) REVERT: B 22 ARG cc_start: 0.7207 (mtt180) cc_final: 0.6808 (mtt180) REVERT: B 128 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 197 ARG cc_start: 0.7268 (mpt-90) cc_final: 0.6930 (mtt-85) REVERT: B 214 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.7077 (mmt180) REVERT: B 219 ARG cc_start: 0.7996 (mtp85) cc_final: 0.7698 (mtt-85) REVERT: B 258 ASP cc_start: 0.7778 (t0) cc_final: 0.7044 (t0) REVERT: R 37 LEU cc_start: 0.7141 (tp) cc_final: 0.6767 (tm) REVERT: R 41 PHE cc_start: 0.7835 (m-80) cc_final: 0.7488 (m-80) REVERT: R 51 LEU cc_start: 0.8324 (mt) cc_final: 0.8098 (mt) REVERT: R 55 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7947 (tt) REVERT: R 82 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8627 (mm) REVERT: R 105 MET cc_start: 0.7391 (mmm) cc_final: 0.7007 (mmm) REVERT: R 121 MET cc_start: 0.8041 (tpp) cc_final: 0.7577 (mpp) REVERT: R 204 ILE cc_start: 0.8408 (pp) cc_final: 0.8175 (pt) REVERT: R 235 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7449 (mmmm) REVERT: R 275 SER cc_start: 0.8428 (t) cc_final: 0.7763 (m) REVERT: R 299 ILE cc_start: 0.8476 (mt) cc_final: 0.8243 (tt) REVERT: S 39 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7542 (tp40) REVERT: S 98 ARG cc_start: 0.8731 (ptm160) cc_final: 0.8455 (ptm160) REVERT: S 150 SER cc_start: 0.8766 (t) cc_final: 0.8458 (p) REVERT: S 223 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7732 (t80) outliers start: 35 outliers final: 24 residues processed: 264 average time/residue: 1.0966 time to fit residues: 309.7515 Evaluate side-chains 281 residues out of total 989 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 251 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain R residue 55 LEU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 183 CYS Chi-restraints excluded: chain R residue 235 LYS Chi-restraints excluded: chain R residue 298 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 39 GLN Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 167 GLN Chi-restraints excluded: chain S residue 223 TYR 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: 0.9980 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 311 ASN B 35 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.109155 restraints weight = 13069.892| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.98 r_work: 0.3293 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9193 Z= 0.231 Angle : 0.551 11.799 12444 Z= 0.279 Chirality : 0.042 0.367 1414 Planarity : 0.003 0.063 1558 Dihedral : 5.904 70.015 1245 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.44 % Allowed : 30.36 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.25), residues: 1125 helix: 2.38 (0.26), residues: 402 sheet: 0.29 (0.30), residues: 290 loop : -0.66 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 251 HIS 0.005 0.001 HIS S 35 PHE 0.026 0.002 PHE S 68 TYR 0.011 0.001 TYR R 114 ARG 0.004 0.000 ARG S 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4947.04 seconds wall clock time: 88 minutes 24.37 seconds (5304.37 seconds total)