Starting phenix.real_space_refine on Wed Feb 14 08:47:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7euo_31323/02_2024/7euo_31323_updated.pdb" } resolution = 2.9 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= 0.072 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 64 5.16 5 C 5732 2.51 5 N 1511 2.21 5 O 1643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 267": "NH1" <-> "NH2" Residue "R ARG 269": "NH1" <-> "NH2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 160": "NH1" <-> "NH2" Residue "S GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2323 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 12, 'TRANS': 282} Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Classifications: {'peptide': 3} Modifications used: {'COO': 1} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.29, per 1000 atoms: 0.59 Number of scatterers: 8950 At special positions: 0 Unit cell: (88.4, 124.95, 123.25, 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 64 16.00 O 1643 8.00 N 1511 7.00 C 5732 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 98 " - pdb=" SG CYS R 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 3.17 Conformation dependent library (CDL) restraints added in 1.8 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 14 sheets defined 34.5% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'R' and resid 23 through 52 removed outlier: 3.734A pdb=" N ILE R 27 " --> pdb=" O LEU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 87 removed outlier: 3.788A pdb=" N LEU R 78 " --> pdb=" O PHE R 74 " (cutoff:3.500A) Proline residue: R 79 - end of helix Processing helix chain 'R' and resid 95 through 128 Processing helix chain 'R' and resid 130 through 135 removed outlier: 3.735A pdb=" N ASN R 135 " --> pdb=" O VAL R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 145 Processing helix chain 'R' and resid 147 through 163 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 187 through 208 Processing helix chain 'R' and resid 211 through 231 Processing helix chain 'R' and resid 238 through 266 Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 268 through 273 removed outlier: 3.882A pdb=" N GLN R 273 " --> pdb=" O ARG R 269 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 301 removed outlier: 3.821A pdb=" N ASP R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN R 293 " --> pdb=" O LEU R 289 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER R 294 " --> pdb=" O ALA R 290 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N CYS R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Proline residue: R 298 - end of helix Processing helix chain 'R' and resid 306 through 315 Processing helix chain 'A' and resid 9 through 32 removed outlier: 4.530A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 5.582A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 274 through 280 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: 4.016A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 164 through 168 Processing sheet with id= B, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.469A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.804A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.942A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.857A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.852A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.750A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.650A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.894A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.551A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.599A pdb=" N LYS S 244 " --> pdb=" O VAL S 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= N, first strand: chain 'S' and resid 225 through 231 removed outlier: 6.216A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1176 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: 2.72 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1444 1.32 - 1.44: 2509 1.44 - 1.57: 5095 1.57 - 1.70: 1 1.70 - 1.82: 95 Bond restraints: 9144 Sorted by residual: bond pdb=" CA SER B 281 " pdb=" C SER B 281 " ideal model delta sigma weight residual 1.522 1.474 0.047 1.31e-02 5.83e+03 1.29e+01 bond pdb=" C ILE R 204 " pdb=" O ILE R 204 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" CA SER B 281 " pdb=" CB SER B 281 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.60e-02 3.91e+03 1.13e+01 bond pdb=" N ILE R 207 " pdb=" CA ILE R 207 " ideal model delta sigma weight residual 1.459 1.418 0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.26e-02 6.30e+03 9.74e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 98.03 - 105.23: 149 105.23 - 112.43: 4733 112.43 - 119.63: 2896 119.63 - 126.83: 4493 126.83 - 134.04: 124 Bond angle restraints: 12395 Sorted by residual: angle pdb=" N ARG R 201 " pdb=" CA ARG R 201 " pdb=" C ARG R 201 " ideal model delta sigma weight residual 111.14 107.05 4.09 1.08e+00 8.57e-01 1.44e+01 angle pdb=" O ILE R 203 " pdb=" C ILE R 203 " pdb=" N ILE R 204 " ideal model delta sigma weight residual 121.83 118.40 3.43 1.03e+00 9.43e-01 1.11e+01 angle pdb=" N LEU R 78 " pdb=" CA LEU R 78 " pdb=" C LEU R 78 " ideal model delta sigma weight residual 109.81 116.69 -6.88 2.21e+00 2.05e-01 9.68e+00 angle pdb=" CA PRO A 282 " pdb=" N PRO A 282 " pdb=" CD PRO A 282 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 angle pdb=" C ILE R 207 " pdb=" N ILE R 208 " pdb=" CA ILE R 208 " ideal model delta sigma weight residual 122.35 118.85 3.50 1.18e+00 7.18e-01 8.78e+00 ... (remaining 12390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 4983 17.93 - 35.87: 430 35.87 - 53.80: 70 53.80 - 71.74: 11 71.74 - 89.67: 7 Dihedral angle restraints: 5501 sinusoidal: 2219 harmonic: 3282 Sorted by residual: dihedral pdb=" CA GLU B 215 " pdb=" C GLU B 215 " pdb=" N GLY B 216 " pdb=" CA GLY B 216 " ideal model delta harmonic sigma weight residual 180.00 157.91 22.09 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR S 101 " pdb=" C TYR S 101 " pdb=" N TYR S 102 " pdb=" CA TYR S 102 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1346 0.097 - 0.195: 66 0.195 - 0.292: 3 0.292 - 0.389: 2 0.389 - 0.486: 2 Chirality restraints: 1419 Sorted by residual: chirality pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C15 CLR R 402 " pdb=" C8 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.49 2.00e-01 2.50e+01 5.91e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C10 CLR R 402 " pdb=" C1 CLR R 402 " pdb=" C5 CLR R 402 " pdb=" C9 CLR R 402 " both_signs ideal model delta sigma weight residual False -2.85 -2.49 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 1416 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 203 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ILE R 203 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE R 203 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE R 204 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 280 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.97e+00 pdb=" C LYS B 280 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS B 280 " -0.018 2.00e-02 2.50e+03 pdb=" N SER B 281 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 281 " 0.040 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 282 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " 0.032 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 709 2.74 - 3.28: 8704 3.28 - 3.82: 13918 3.82 - 4.36: 16097 4.36 - 4.90: 29474 Nonbonded interactions: 68902 Sorted by model distance: nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.198 2.440 nonbonded pdb=" NH1 ARG B 251 " pdb=" OE2 GLU B 260 " model vdw 2.270 2.520 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.274 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.276 2.440 nonbonded pdb=" OD2 ASP R 186 " pdb=" NZ LYS R 188 " model vdw 2.282 2.520 ... (remaining 68897 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: 1.360 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: 4.090 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 27.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 45.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 0.090 9144 Z= 0.246 Angle : 0.648 8.155 12395 Z= 0.355 Chirality : 0.051 0.486 1419 Planarity : 0.004 0.059 1550 Dihedral : 13.715 89.671 3374 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1119 helix: 1.83 (0.27), residues: 387 sheet: -0.53 (0.29), residues: 286 loop : -1.65 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 211 HIS 0.013 0.001 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.003 0.000 ARG S 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8604 (m170) cc_final: 0.8366 (m-70) REVERT: A 193 ASP cc_start: 0.8488 (m-30) cc_final: 0.8254 (m-30) REVERT: A 242 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7757 (mmt90) REVERT: G 58 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8320 (mp0) REVERT: S 160 ARG cc_start: 0.7788 (ttp80) cc_final: 0.7360 (ttm110) REVERT: S 234 GLU cc_start: 0.7925 (pt0) cc_final: 0.7262 (pp20) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 1.1228 time to fit residues: 202.4547 Evaluate side-chains 119 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 0.0040 overall best weight: 1.6154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 259 GLN B 268 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9144 Z= 0.245 Angle : 0.564 6.690 12395 Z= 0.295 Chirality : 0.042 0.138 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.644 78.924 1356 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.17 % Allowed : 10.73 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.25), residues: 1119 helix: 1.96 (0.26), residues: 394 sheet: -0.53 (0.29), residues: 293 loop : -1.55 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.009 0.001 HIS S 35 PHE 0.015 0.001 PHE R 24 TYR 0.012 0.001 TYR S 190 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 257 TYR cc_start: 0.7931 (t80) cc_final: 0.7673 (t80) REVERT: A 193 ASP cc_start: 0.8500 (m-30) cc_final: 0.8268 (m-30) REVERT: A 309 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: B 217 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6716 (ptp) REVERT: G 58 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8343 (mp0) REVERT: S 160 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7425 (ttm110) REVERT: S 234 GLU cc_start: 0.8015 (pt0) cc_final: 0.7292 (pp20) outliers start: 21 outliers final: 11 residues processed: 133 average time/residue: 1.1589 time to fit residues: 165.1221 Evaluate side-chains 127 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS S 77 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9144 Z= 0.150 Angle : 0.499 6.758 12395 Z= 0.260 Chirality : 0.040 0.135 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.355 75.642 1356 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.17 % Allowed : 13.83 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1119 helix: 2.24 (0.27), residues: 387 sheet: -0.42 (0.29), residues: 294 loop : -1.45 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.008 0.001 HIS S 35 PHE 0.011 0.001 PHE R 24 TYR 0.011 0.001 TYR S 190 ARG 0.008 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8587 (m170) cc_final: 0.8358 (m-70) REVERT: R 87 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.7078 (mpt) REVERT: R 257 TYR cc_start: 0.7877 (t80) cc_final: 0.7603 (t80) REVERT: R 306 GLN cc_start: 0.7717 (tp40) cc_final: 0.7510 (mm-40) REVERT: A 193 ASP cc_start: 0.8497 (m-30) cc_final: 0.8271 (m-30) REVERT: A 242 ARG cc_start: 0.7383 (mmt90) cc_final: 0.6638 (mmt90) REVERT: A 309 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: G 58 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8314 (mp0) REVERT: S 160 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7329 (ttm110) REVERT: S 234 GLU cc_start: 0.7956 (pt0) cc_final: 0.7227 (pp20) outliers start: 21 outliers final: 8 residues processed: 141 average time/residue: 1.1387 time to fit residues: 172.1173 Evaluate side-chains 126 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain S residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 60 optimal weight: 4.9990 overall best weight: 1.8824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9144 Z= 0.274 Angle : 0.557 7.677 12395 Z= 0.292 Chirality : 0.042 0.134 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.483 73.119 1356 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.99 % Allowed : 15.69 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1119 helix: 2.14 (0.27), residues: 389 sheet: -0.47 (0.29), residues: 299 loop : -1.40 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.014 0.001 PHE A 189 TYR 0.009 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 87 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7134 (mpt) REVERT: R 257 TYR cc_start: 0.7957 (t80) cc_final: 0.7736 (t80) REVERT: R 306 GLN cc_start: 0.7715 (tp40) cc_final: 0.7487 (mm-40) REVERT: A 193 ASP cc_start: 0.8508 (m-30) cc_final: 0.8266 (m-30) REVERT: A 309 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: B 130 GLU cc_start: 0.8314 (mp0) cc_final: 0.8103 (mp0) REVERT: B 215 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7509 (pp20) REVERT: B 217 MET cc_start: 0.8068 (ptt) cc_final: 0.7591 (ptm) REVERT: G 46 LYS cc_start: 0.9195 (mppt) cc_final: 0.8840 (mtmm) REVERT: G 47 GLU cc_start: 0.8179 (mp0) cc_final: 0.7939 (mp0) REVERT: G 58 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8286 (mp0) REVERT: S 160 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7475 (ttm110) REVERT: S 234 GLU cc_start: 0.8050 (pt0) cc_final: 0.7322 (pp20) outliers start: 29 outliers final: 17 residues processed: 135 average time/residue: 1.1375 time to fit residues: 164.7213 Evaluate side-chains 129 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 119 VAL Chi-restraints excluded: chain C residue 2 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9144 Z= 0.212 Angle : 0.529 6.712 12395 Z= 0.277 Chirality : 0.041 0.134 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.365 69.797 1356 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.61 % Allowed : 16.00 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1119 helix: 2.16 (0.27), residues: 389 sheet: -0.35 (0.29), residues: 293 loop : -1.41 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.012 0.001 PHE A 189 TYR 0.009 0.001 TYR S 190 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 112 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8578 (m170) cc_final: 0.8364 (m-70) REVERT: R 87 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7080 (mpt) REVERT: R 257 TYR cc_start: 0.7908 (t80) cc_final: 0.7687 (t80) REVERT: A 193 ASP cc_start: 0.8494 (m-30) cc_final: 0.8260 (m-30) REVERT: A 309 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7836 (m-30) REVERT: B 215 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7670 (pp20) REVERT: B 217 MET cc_start: 0.8005 (ptt) cc_final: 0.7645 (ptm) REVERT: G 46 LYS cc_start: 0.9180 (mppt) cc_final: 0.8852 (mtmm) REVERT: G 58 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8285 (mp0) REVERT: S 160 ARG cc_start: 0.7908 (ttp80) cc_final: 0.7469 (ttm110) REVERT: S 234 GLU cc_start: 0.8025 (pt0) cc_final: 0.7286 (pp20) outliers start: 35 outliers final: 19 residues processed: 134 average time/residue: 1.2111 time to fit residues: 173.4533 Evaluate side-chains 131 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 87 MET Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 241 ASN B 268 ASN ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9144 Z= 0.165 Angle : 0.520 11.152 12395 Z= 0.266 Chirality : 0.040 0.131 1419 Planarity : 0.003 0.038 1550 Dihedral : 5.200 64.971 1356 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.30 % Allowed : 17.44 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1119 helix: 2.16 (0.27), residues: 394 sheet: -0.34 (0.29), residues: 294 loop : -1.36 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.008 0.001 TYR S 190 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 118 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8555 (m170) cc_final: 0.8343 (m-70) REVERT: R 257 TYR cc_start: 0.7917 (t80) cc_final: 0.7695 (t80) REVERT: R 306 GLN cc_start: 0.7689 (mm-40) cc_final: 0.6738 (tm-30) REVERT: A 193 ASP cc_start: 0.8495 (m-30) cc_final: 0.8263 (m-30) REVERT: A 309 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: B 217 MET cc_start: 0.7954 (ptt) cc_final: 0.7661 (ptp) REVERT: G 46 LYS cc_start: 0.9172 (mppt) cc_final: 0.8837 (mtmm) REVERT: G 47 GLU cc_start: 0.8156 (mp0) cc_final: 0.7913 (mp0) REVERT: G 58 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8273 (mp0) REVERT: S 160 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7424 (ttm110) REVERT: S 234 GLU cc_start: 0.7989 (pt0) cc_final: 0.7251 (pp20) outliers start: 32 outliers final: 21 residues processed: 140 average time/residue: 1.1874 time to fit residues: 178.1408 Evaluate side-chains 135 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.0870 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9144 Z= 0.149 Angle : 0.512 10.151 12395 Z= 0.262 Chirality : 0.040 0.137 1419 Planarity : 0.003 0.039 1550 Dihedral : 5.081 59.197 1356 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.79 % Allowed : 18.06 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.26), residues: 1119 helix: 2.18 (0.27), residues: 394 sheet: -0.25 (0.30), residues: 289 loop : -1.35 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE A 189 TYR 0.008 0.001 TYR S 190 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8520 (m170) cc_final: 0.8307 (m-70) REVERT: R 257 TYR cc_start: 0.7934 (t80) cc_final: 0.7711 (t80) REVERT: A 193 ASP cc_start: 0.8492 (m-30) cc_final: 0.8263 (m-30) REVERT: B 130 GLU cc_start: 0.8298 (mp0) cc_final: 0.7732 (mp0) REVERT: B 217 MET cc_start: 0.7848 (ptt) cc_final: 0.7376 (ppp) REVERT: G 46 LYS cc_start: 0.9154 (mppt) cc_final: 0.8856 (mtmm) REVERT: S 160 ARG cc_start: 0.7829 (ttp80) cc_final: 0.7378 (ttm110) REVERT: S 234 GLU cc_start: 0.8000 (pt0) cc_final: 0.7276 (pp20) outliers start: 27 outliers final: 20 residues processed: 135 average time/residue: 1.1829 time to fit residues: 171.2918 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.0670 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 93 optimal weight: 0.0070 chunk 99 optimal weight: 0.8980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 90 HIS ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9144 Z= 0.133 Angle : 0.503 8.869 12395 Z= 0.256 Chirality : 0.039 0.137 1419 Planarity : 0.003 0.039 1550 Dihedral : 4.889 50.390 1356 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.58 % Allowed : 19.61 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1119 helix: 2.28 (0.27), residues: 392 sheet: -0.20 (0.30), residues: 289 loop : -1.23 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.011 0.001 PHE R 24 TYR 0.008 0.001 TYR S 190 ARG 0.004 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8460 (m170) cc_final: 0.8242 (m-70) REVERT: R 87 MET cc_start: 0.8475 (tpp) cc_final: 0.7934 (mtt) REVERT: R 257 TYR cc_start: 0.7930 (t80) cc_final: 0.7699 (t80) REVERT: A 193 ASP cc_start: 0.8481 (m-30) cc_final: 0.8252 (m-30) REVERT: A 309 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7848 (m-30) REVERT: B 130 GLU cc_start: 0.8312 (mp0) cc_final: 0.7725 (mp0) REVERT: B 217 MET cc_start: 0.7785 (ptt) cc_final: 0.7355 (ppp) REVERT: G 46 LYS cc_start: 0.9156 (mppt) cc_final: 0.8832 (mtmm) REVERT: G 47 GLU cc_start: 0.8034 (mp0) cc_final: 0.7817 (mp0) REVERT: S 160 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7388 (ttm110) REVERT: S 234 GLU cc_start: 0.7970 (pt0) cc_final: 0.7248 (pp20) outliers start: 25 outliers final: 18 residues processed: 142 average time/residue: 1.1096 time to fit residues: 169.2929 Evaluate side-chains 133 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.183 Angle : 0.526 8.311 12395 Z= 0.270 Chirality : 0.040 0.133 1419 Planarity : 0.003 0.039 1550 Dihedral : 4.908 43.909 1356 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.89 % Allowed : 19.61 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1119 helix: 2.29 (0.27), residues: 392 sheet: -0.17 (0.30), residues: 284 loop : -1.23 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.024 0.001 PHE R 74 TYR 0.008 0.001 TYR S 190 ARG 0.006 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8536 (m170) cc_final: 0.8335 (m-70) REVERT: R 257 TYR cc_start: 0.7936 (t80) cc_final: 0.7686 (t80) REVERT: A 193 ASP cc_start: 0.8484 (m-30) cc_final: 0.8252 (m-30) REVERT: A 309 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: B 130 GLU cc_start: 0.8293 (mp0) cc_final: 0.7696 (mp0) REVERT: B 217 MET cc_start: 0.7817 (ptt) cc_final: 0.7298 (ppp) REVERT: G 46 LYS cc_start: 0.9162 (mppt) cc_final: 0.8839 (mtmm) REVERT: G 47 GLU cc_start: 0.8008 (mp0) cc_final: 0.7771 (mp0) REVERT: S 43 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8150 (mttp) REVERT: S 160 ARG cc_start: 0.7928 (ttp80) cc_final: 0.7499 (ttm110) REVERT: S 234 GLU cc_start: 0.8018 (pt0) cc_final: 0.7303 (pp20) outliers start: 28 outliers final: 23 residues processed: 139 average time/residue: 1.2490 time to fit residues: 186.2561 Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 20.0000 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 overall best weight: 1.1920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS B 268 ASN ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.196 Angle : 0.535 7.962 12395 Z= 0.273 Chirality : 0.040 0.132 1419 Planarity : 0.003 0.039 1550 Dihedral : 4.906 37.113 1356 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.58 % Allowed : 20.23 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1119 helix: 2.29 (0.27), residues: 394 sheet: -0.24 (0.30), residues: 289 loop : -1.19 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.024 0.001 PHE R 74 TYR 0.008 0.001 TYR S 102 ARG 0.003 0.000 ARG A 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 HIS cc_start: 0.8568 (m170) cc_final: 0.8356 (m-70) REVERT: R 257 TYR cc_start: 0.7949 (t80) cc_final: 0.7702 (t80) REVERT: A 193 ASP cc_start: 0.8469 (m-30) cc_final: 0.8235 (m-30) REVERT: A 242 ARG cc_start: 0.7288 (mmt90) cc_final: 0.6792 (mmm-85) REVERT: A 309 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: B 130 GLU cc_start: 0.8288 (mp0) cc_final: 0.7689 (mp0) REVERT: B 217 MET cc_start: 0.7761 (ptt) cc_final: 0.7246 (ppp) REVERT: G 46 LYS cc_start: 0.9169 (mppt) cc_final: 0.8843 (mtmm) REVERT: G 47 GLU cc_start: 0.8013 (mp0) cc_final: 0.7740 (mp0) REVERT: S 160 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7507 (ttm110) REVERT: S 234 GLU cc_start: 0.8029 (pt0) cc_final: 0.7316 (pp20) REVERT: C 2 LEU cc_start: 0.7678 (pp) cc_final: 0.7473 (pp) outliers start: 25 outliers final: 24 residues processed: 133 average time/residue: 1.1988 time to fit residues: 170.9368 Evaluate side-chains 139 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 98 CYS Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 174 VAL Chi-restraints excluded: chain R residue 229 HIS Chi-restraints excluded: chain R residue 240 LEU Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 310 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** S 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.131537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.088560 restraints weight = 11899.247| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.18 r_work: 0.2972 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9144 Z= 0.174 Angle : 0.525 7.718 12395 Z= 0.268 Chirality : 0.040 0.134 1419 Planarity : 0.003 0.040 1550 Dihedral : 4.831 36.397 1356 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.79 % Allowed : 20.02 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.25), residues: 1119 helix: 2.31 (0.27), residues: 393 sheet: -0.18 (0.30), residues: 288 loop : -1.22 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.006 0.001 HIS S 35 PHE 0.024 0.001 PHE R 74 TYR 0.008 0.001 TYR S 102 ARG 0.004 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3520.37 seconds wall clock time: 63 minutes 19.67 seconds (3799.67 seconds total)